Hi Tim,
Thanks a lot for pointing that out!
Here is the IDXREF-output from XDS, without input of unit cell constants.
Sabine
***** DETERMINATION OF THE RECIPROCAL LATTICE BASIS ******
NUMBER OF DIFFERENCE VECTOR CLUSTERS USED 200
MAXIMUM RADIUS OF DIFFERENCE VECTOR CLUSTERS (pixels) 3
MINIMUM DISTANCE BETWEEN DIFFRACTION SPOTS (pixel) 6.0
MINIMUM ALLOWED DISTANCE BETWEEN REC. LATTICE POINTS 0.2682E-02
OBSERVED BASIS CELL VOLUME 0.5948E+06
DIMENSION OF SPACE SPANNED BY DIFFERENCE VECTOR CLUSTERS 3
# COORDINATES OF REC. BASIS VECTOR LENGTH 1/LENGTH
1 0.0001394 0.0087644-0.0025818 0.0091378 109.44
2 0.0099426 0.0011533 0.0044729 0.0109632 91.21
3 0.0070894-0.0044146-0.0145563 0.0167819 59.59
CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS
VECTORS
# COORDINATES OF VECTOR CLUSTER FREQUENCY CLUSTER INDICES
1 -0.0198775-0.0023086-0.0089462 3033. -0.00 -2.00 0.00
2 0.0170296-0.0032635-0.0100896 2931. -0.00 1.00 1.00
3 -0.0028512-0.0055653-0.0190257 2769. 0.00 -1.00 1.00
4 0.0001345 0.0087600-0.0025802 2756. 1.00 -0.00 -0.00
5 -0.0099406-0.0011518-0.0044669 2748. -0.00 -1.00 -0.00
6 0.0369226-0.0009571-0.0011409 2572. -0.00 3.00 1.00
7 -0.0027157 0.0031989-0.0215974 2517. 1.00 -1.00 1.00
8 0.0102242 0.0186700-0.0006904 2503. 2.00 1.00 0.00
9 -0.0098018 0.0076072-0.0070529 2471. 1.00 -1.00 0.00
10 0.0096649-0.0163634 0.0096361 2465. -2.00 1.00 -0.00
11 -0.0171648-0.0055039 0.0126657 2460. -1.00 -1.00 -1.00
12 -0.0070927 0.0044138 0.0145582 2456. -0.00 -0.00 -1.00
13 0.0072273 0.0043496-0.0171271 2446. 1.00 0.00 1.00
14 0.0068016-0.0219329-0.0093878 2437. -2.00 -0.00 1.00
15 0.0197453-0.0064538 0.0115256 2428. -1.00 2.00 0.00
16 0.0100947 0.0099143 0.0018904 2413. 1.00 1.00 0.00
17 0.0073643 0.0131126-0.0197118 2403. 2.00 -0.00 1.00
18 0.0397690 0.0046107 0.0178903 2388. -0.00 4.00 0.00
19 0.0227406 0.0078707 0.0279747 2383. -0.00 3.00 -1.00
20 -0.0141824 0.0088224 0.0291127 2383. -0.00 -0.00 -2.00
21 0.0103597 0.0274362-0.0032718 2361. 3.00 1.00 0.00
22 -0.0269727 0.0021092 0.0056176 2346. -0.00 -2.00 -1.00
23 0.0340618-0.0065201-0.0201693 2329. 0.00 2.00 2.00
24 -0.0200231-0.0110674-0.0063643 2326. -1.00 -2.00 0.00
25 0.0125162-0.0108063 0.0286538 2325. -2.00 2.00 -1.00
26 -0.0126463 0.0020440-0.0260664 2323. 1.00 -2.00 1.00
27 0.0143145-0.0000672-0.0316916 2308. 1.00 -0.00 2.00
28 0.0168948-0.0120237-0.0075083 2306. -1.00 1.00 1.00
29 0.0066708-0.0307011-0.0068110 2284. -3.00 0.00 1.00
30 0.0002795 0.0175230-0.0051646 2283. 2.00 -0.00 0.00
31 -0.0226058 0.0008922-0.0305478 2283. 1.00 -3.00 1.00
32 0.0095181-0.0251297 0.0122100 2276. -3.00 1.00 0.00
33 -0.0029959-0.0143306-0.0164454 2250. -1.00 -1.00 1.00
34 0.0130704 0.0242365 0.0183371 2229. 2.00 2.00 -1.00
35 0.0267005-0.0196259-0.0004455 2214. -2.00 2.00 1.00
36 -0.0057125-0.0111320-0.0380540 2212. 0.00 -2.00 2.00
37 0.0127956 0.0067207 0.0235036 2195. -0.00 2.00 -1.00
38 0.0272584 0.0154143-0.0107700 2194. 2.00 2.00 1.00
39 0.0075127 0.0218694-0.0222930 2180. 3.00 0.00 1.00
40 0.0045134 0.0075431-0.0387461 2180. 2.00 -1.00 2.00
41 0.0298233 0.0034561 0.0134186 2169. -0.00 3.00 -0.00
42 0.0271311 0.0066555-0.0081839 2159. 1.00 2.00 1.00
43 -0.0242614-0.0010891 0.0272244 2138. -1.00 -1.00 -2.00
44 0.0341972 0.0022350-0.0227552 2121. 1.00 2.00 2.00
45 -0.0043753 0.0012122 0.0361620 2118. -1.00 1.00 -2.00
46 0.0244151 0.0098478-0.0298116 2112. 2.00 1.00 2.00
47 -0.0055691-0.0023701-0.0406352 2104. 1.00 -2.00 2.00
48 -0.0301120-0.0209742-0.0082509 2090. -2.00 -3.00 -0.00
49 -0.0296785 0.0052997-0.0159965 2086. 1.00 -3.00 0.00
50 -0.0268292 0.0108693 0.0030314 2076. 1.00 -2.00 -1.00
51 -0.0004199-0.0262847 0.0077376 2066. -3.00 -0.00 0.00
52 0.0132169 0.0330109 0.0157589 2061. 3.00 2.00 -1.00
53 -0.0005534-0.0350474 0.0103260 2049. -4.00 0.00 0.00
54 -0.0123845 0.0195574-0.0312418 2043. 3.00 -2.00 1.00
55 -0.0201672-0.0198288-0.0037871 2039. -2.00 -2.00 0.00
56 -0.0007071-0.0438227 0.0129006 2026. -5.00 -0.00 0.00
57 -0.0025795 0.0119525-0.0241882 2025. 2.00 -1.00 1.00
58 0.0396384-0.0041547 0.0204763 2025. -1.00 4.00 0.00
59 0.0196131-0.0152142 0.0141121 2020. -2.00 2.00 -0.00
60 -0.0241198 0.0076707 0.0246372 2014. -0.00 -1.00 -2.00
PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES)
59.59 91.21 109.44 90.03 90.05 90.09
# COORDINATES OF REC. BASIS VECTOR REDUCED CELL INDICES
1 0.0001394 0.0087644-0.0025818 0.00 -0.00 -1.00
2 0.0099426 0.0011533 0.0044729 0.00 1.00 0.00
3 0.0070894-0.0044146-0.0145563 1.00 -0.00 0.00
LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES)
CHARACTER LATTICE OF FIT a b c alpha beta gamma
* 44 aP 0.0 59.9 91.6 110.0 90.0 90.0 90.0
* 31 aP 0.4 59.9 91.6 110.0 90.0 90.0 90.0
* 33 mP 0.9 59.9 91.6 110.0 90.0 90.0 90.0
* 34 mP 1.1 59.9 110.0 91.6 90.0 90.0 90.0
* 35 mP 1.2 91.6 59.9 110.0 90.0 90.0 90.0
* 32 oP 1.6 59.9 91.6 110.0 90.0 90.0 90.0
37 mC 249.7 227.9 59.9 91.6 90.0 90.0 74.8
36 oC 250.1 59.9 227.9 91.6 90.0 90.0 105.2
39 mC 250.3 192.7 59.9 110.0 90.0 90.0 71.9
28 mC 250.3 59.9 227.9 91.6 90.0 90.0 74.8
38 oC 250.7 59.9 192.7 110.0 90.0 90.0 108.1
------------------------------------------
Dr. Sabine Schneider
Research Group Leader
Technical University of Munich
Department of Chemistry
Chair of Biochemistry
Lichtenbergstr. 4
85748 Garching
Germany
Tel.: +49 (0) 89 289 13336
Fax: +49 (0) 89 289 13363
http://www.biochemie.ch.tum.de/index.php?id=919
On 11/17/2016 08:56 AM, Tim Gruene wrote:
> Hi Sabine,
>
> your reduced cell angles are exactly 90 degree. This seems unusual to me. Do
> you specify the unit cell constants in XDS.INP, including a space group, or do
> you leave the space group undefined? In the former case I am unsure if your
> list of clusters may be biased, although it might contain half integers in
> that case.
>
> Best,
> Tim
>
> On Thursday, November 17, 2016 08:37:07 AM Sabine Schneider wrote:
>> Hello Kay,
>>
>> I'd say yes, but I might miss something.
>>
>> Here is the IDXREF.LP output:
>>
>> Sabine
>>
>>
>> ***** DETERMINATION OF THE RECIPROCAL LATTICE BASIS ******
>> NUMBER OF DIFFERENCE VECTOR CLUSTERS USED 200
>> MAXIMUM RADIUS OF DIFFERENCE VECTOR CLUSTERS (pixels) 3
>> MINIMUM DISTANCE BETWEEN DIFFRACTION SPOTS (pixel) 6.0
>> MINIMUM ALLOWED DISTANCE BETWEEN REC. LATTICE POINTS 0.2682E-02
>> OBSERVED BASIS CELL VOLUME 0.6021E+06
>> DIMENSION OF SPACE SPANNED BY DIFFERENCE VECTOR CLUSTERS 3
>>
>> # COORDINATES OF REC. BASIS VECTOR LENGTH 1/LENGTH
>>
>> 1 0.0070481-0.0043879-0.0144998 0.0167084 59.85
>> 2 0.0099022 0.0011565 0.0044633 0.0109230 91.55
>> 3 -0.0001404-0.0087276 0.0025729 0.0091000 109.89
>>
>> CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS
>>
>> # COORDINATES OF VECTOR CLUSTER FREQUENCY CLUSTER INDICES
>> 1 -0.0198775-0.0023086-0.0089462 3033. -0.00 -2.01 -0.00
>> 2 0.0170296-0.0032635-0.0100896 2931. 1.01 1.00 0.00
>> 3 -0.0028512-0.0055653-0.0190257 2769. 1.00 -1.00 0.00
>> 4 0.0001345 0.0087600-0.0025802 2756. -0.00 -0.00 -1.00
>> 5 -0.0099406-0.0011518-0.0044669 2748. -0.00 -1.00 -0.00
>> 6 0.0369226-0.0009571-0.0011409 2572. 1.01 3.01 0.00
>> 7 -0.0027157 0.0031989-0.0215974 2517. 1.00 -1.00 -1.00
>> 8 0.0102242 0.0186700-0.0006904 2503. 0.00 1.00 -2.01
>> 9 -0.0098018 0.0076072-0.0070529 2471. -0.00 -1.00 -1.00
>> 10 0.0096649-0.0163634 0.0096361 2465. 0.00 1.00 2.01
>> 11 -0.0171648-0.0055039 0.0126657 2460. -1.00 -1.00 1.00
>> 12 -0.0070927 0.0044138 0.0145582 2456. -1.00 -0.00 -0.00
>> 13 0.0072273 0.0043496-0.0171271 2446. 1.00 0.00 -1.00
>> 14 0.0068016-0.0219329-0.0093878 2437. 1.00 0.00 2.01
>> 15 0.0197453-0.0064538 0.0115256 2428. 0.00 2.01 1.00
>> 16 0.0100947 0.0099143 0.0018904 2413. 0.00 1.00 -1.00
>> 17 0.0073643 0.0131126-0.0197118 2403. 1.00 0.00 -2.01
>> 18 0.0397690 0.0046107 0.0178903 2388. 0.00 4.01 0.00
>> 19 0.0227406 0.0078707 0.0279747 2383. -1.00 3.01 0.00
>> 20 -0.0141824 0.0088224 0.0291127 2383. -2.01 -0.00 -0.00
>> 21 0.0103597 0.0274362-0.0032718 2361. 0.00 1.00 -3.01
>> 22 -0.0269727 0.0021092 0.0056176 2346. -1.01 -2.01 -0.00
>> 23 0.0340618-0.0065201-0.0201693 2329. 2.01 2.01 0.00
>> 24 -0.0200231-0.0110674-0.0063643 2326. -0.00 -2.01 1.00
>> 25 0.0125162-0.0108063 0.0286538 2325. -1.00 2.01 2.01
>> 26 -0.0126463 0.0020440-0.0260664 2323. 1.00 -2.00 -1.00
>> 27 0.0143145-0.0000672-0.0316916 2308. 2.01 0.00 -1.00
>> 28 0.0168948-0.0120237-0.0075083 2306. 1.01 1.00 1.01
>> 29 0.0066708-0.0307011-0.0068110 2284. 1.00 0.00 3.01
>> 30 0.0002795 0.0175230-0.0051646 2283. -0.00 -0.00 -2.01
>> 31 -0.0226058 0.0008922-0.0305478 2283. 1.00 -3.01 -1.00
>> 32 0.0095181-0.0251297 0.0122100 2276. 0.00 1.00 3.01
>> 33 -0.0029959-0.0143306-0.0164454 2250. 1.00 -1.00 1.00
>> 34 0.0130704 0.0242365 0.0183371 2229. -1.00 2.01 -2.01
>> 35 0.0267005-0.0196259-0.0004455 2214. 1.01 2.01 2.01
>> 36 -0.0057125-0.0111320-0.0380540 2212. 2.01 -2.01 0.00
>> 37 0.0127956 0.0067207 0.0235036 2195. -1.00 2.01 0.00
>> 38 0.0272584 0.0154143-0.0107700 2194. 1.01 2.01 -2.01
>> 39 0.0075127 0.0218694-0.0222930 2180. 1.00 0.00 -3.01
>> 40 0.0045134 0.0075431-0.0387461 2180. 2.01 -1.00 -2.01
>> 41 0.0298233 0.0034561 0.0134186 2169. 0.00 3.01 0.00
>> 42 0.0271311 0.0066555-0.0081839 2159. 1.01 2.01 -1.00
>> 43 -0.0242614-0.0010891 0.0272244 2138. -2.01 -1.01 1.00
>> 44 0.0341972 0.0022350-0.0227552 2121. 2.01 2.01 -1.00
>> 45 -0.0043753 0.0012122 0.0361620 2118. -2.01 1.00 1.00
>> 46 0.0244151 0.0098478-0.0298116 2112. 2.01 1.01 -2.01
>> 47 -0.0055691-0.0023701-0.0406352 2104. 2.01 -2.01 -1.00
>> 48 -0.0301120-0.0209742-0.0082509 2090. -0.00 -3.01 2.01
>> 49 -0.0296785 0.0052997-0.0159965 2086. -0.00 -3.01 -1.01
>> 50 -0.0268292 0.0108693 0.0030314 2076. -1.01 -2.01 -1.01
>> 51 -0.0004199-0.0262847 0.0077376 2066. 0.00 -0.00 3.01
>> 52 0.0132169 0.0330109 0.0157589 2061. -1.00 2.01 -3.01
>> 53 -0.0005534-0.0350474 0.0103260 2049. 0.00 0.00 4.02
>> 54 -0.0123845 0.0195574-0.0312418 2043. 1.00 -2.01 -3.01
>> 55 -0.0201672-0.0198288-0.0037871 2039. -0.00 -2.01 2.01
>> 56 -0.0007071-0.0438227 0.0129006 2026. 0.00 -0.00 5.02
>> 57 -0.0025795 0.0119525-0.0241882 2025. 1.00 -1.00 -2.01
>> 58 0.0396384-0.0041547 0.0204763 2025. 0.00 4.02 1.01
>> 59 0.0196131-0.0152142 0.0141121 2020. 0.00 2.01 2.01
>> 60 -0.0241198 0.0076707 0.0246372 2014. -2.01 -1.01 -0.00
>>
>> PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES)
>> 59.85 91.55 109.89 90.00 90.00 90.00
>>
>> # COORDINATES OF REC. BASIS VECTOR REDUCED CELL INDICES
>>
>> 1 0.0070481-0.0043879-0.0144998 1.00 0.00 0.00
>> 2 0.0099022 0.0011565 0.0044633 0.00 1.00 0.00
>> 3 -0.0001404-0.0087276 0.0025729 0.00 0.00 1.00
>>
>>
>> LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES)
>> CHARACTER LATTICE OF FIT a b c alpha beta gamma
>>
>> * 44 aP 0.0 59.9 91.6 110.0 90.0 90.0 90.0
>> * 31 aP 0.4 59.9 91.6 110.0 90.0 90.0 90.0
>> * 33 mP 0.9 59.9 91.6 110.0 90.0 90.0 90.0
>> * 34 mP 1.1 59.9 110.0 91.6 90.0 90.0 90.0
>> * 35 mP 1.2 91.6 59.9 110.0 90.0 90.0 90.0
>> * 32 oP 1.6 59.9 91.6 110.0 90.0 90.0 90.0
>> 37 mC 249.7 227.9 59.9 91.6 90.0 90.0 74.8
>> 36 oC 250.1 59.9 227.9 91.6 90.0 90.0 105.2
>> 39 mC 250.3 192.7 59.9 110.0 90.0 90.0 71.9
>> 28 mC 250.3 59.9 227.9 91.6 90.0 90.0 74.8
>> 38 oC 250.7 59.9 192.7 110.0 90.0 90.0 108.1
>> 29 mC 250.7 59.9 192.7 110.0 90.0 90.0 71.9
>> 27 mC 500.2 192.8 59.9 143.1 90.1 127.5 71.9
>>
>> On 11/17/2016 08:17 AM, Kay Diederichs wrote:
>>> Hi Sabine,
>>>
>>> my first guess would be that you are overlooking half of the reflections
>>> meaning the cell has really twice the volume. Is the list of difference
>>> vectors in IDXREF.LP clean in this respect?
>>>
>>> Best,
>>>
>>> Kay
>>>
>>> On Wed, 16 Nov 2016 17:26:59 +0100, Sabine Schneider
> <[log in to unmask]> wrote:
>>>> Hello everybody,
>>>>
>>>> I got a problem with solving and refining a structure of a small protein
>>>> of 20kDa, where we just swapped two residue at the surface by mutation
>>>> (AF vs FA).
>>>>
>>>> For the FA variant we got three crystal forms, where we had no problem
>>>> whatsoever with MR and refinement
>>>> - P6522 cell 63 63 184 ~2.9A
>>>> - P21212 cell: 53 62 109 ~3A
>>>> - P212121 cell 40 43 96 ~1.8A
>>>>
>>>> However with the AF-variant we only got one crystal (out of 50) that
>>>> diffracted reasonable well to ~2.4A at the synchrotron. And now the
>>>> problem starts: initially the data appear to be orthorhombic, but:
>>>>
>>>> - SG18/19: cell 59 91 109 (I noticed that the b-axis is longer by 1/2b
>>>> compared to the other variant?!)
>>>> -> running phaser checking all possible alternative SGs found initally 2
>>>> mols/AUS in SG18, but since there was still space (and density!) I let
>>>> it search for another one (increased the clash tolerance)
>>>> SOLU SET RFZ=7.7 TFZ=11.8 PAK=0 LLG=141 TFZ==13.9 RFZ=3.0 TFZ=11.2 PAK=0
>>>> LLG=280 TFZ==17.1 LLG=288 TFZ==17.3 RFZ=5.9 TFZ=16.0 PAK=16 LLG=979
>>>> TFZ==15.3 LLG=1479 TFZ==17.4
>>>>
>>>> - However the third molecule than clashes partly
>>>>
>>>> - running refmac: R/Rfree stays in the high 40
>>>>
>>>> - analysing the data with Xtriage indicates tNCS
>>>>
>>>> - I also tried P212121, P21 and P1, always with the same result: space
>>>> as well as density between the proteins; placing more protein molecules
>>>> results in clashes (i.e. refinement in P1 gives R/Rfree of 38/41)
>>>>
>>>> - data were processed with XDS as well as Dials/Aimless
>>>>
>>>> - the protein is generally well folded, quite stable, without any loose
>>>> ends or flexible regions
>>>>
>>>> - calculation of selfrotation functions in P21 and P21221 gives peak at
>>>> 90dg (kappa=180dg)
>>>>
>>>> Anyone an idea what could be going on or how to solve that?
>>>>
>>>>
>>>> Thanks a lot in advance!
>>>>
>>>> Sabine
|
