" one molecule of 37 kDa with solvent content 17%"
I highly doubt it. It's theoretically possible, but with extremely low
solvent content like this the crystals should be tightly packed, with
all the consequences of tight packing such as higher resolution
diffraction and most of the bits accounted for.
So it's very likely a truncated protein, a wrong space group
assignment or both. That's what makes structural biology fun (and
frustrating).
Artem
On Sat, Jul 16, 2011 at 10:58 PM, Nian Huang <[log in to unmask]> wrote:
> The R and Rfree are low enough so your space group is correct. I don't see a
> resolution in the log file. If it is 3 A dataset, 28% is not bad for a start
> at all. The N terminal region is probably completely disordered if it is not
> degraded.
>
> Nian
>
> On Sat, Jul 16, 2011 at 3:47 AM, Appu kumar <[log in to unmask]> wrote:
>>
>> Dear CCP4 User,
>> I am new to crystallography and i need your
>> valuable suggestion to help me out. We have crystallized full length protein
>> and I am solving protein structure by molecular replacement method and
>> molecular weight of protein is 37kDa. Template pdb i am using have only
>> C-terminal 24kDa protein structure. HKL2000 gave a space group C2221 and
>> Mathews Coefficient indicate one molecule of 37 kDa with solvent content 17%
>> only. When i am running phaser, it gave me a most probable molecualr weight
>> of protein in ASU to be 23kDa. and also i am not getting any density for
>> N-terminal of protein. Right now my Rwrk and Rfree are 28% and 37% but it
>> not decreasing further.
>> When i am indexing in lower symetry sapce group P1211, most probable
>> molecular weight ofpreotin com comes to be 46kDa in ASU. Would please anyone
>> can help, and suggest me what is the real situation?.
>> Thanks in advance
>> Mathews table
>>
>>
>> Data line--- CELL 57.8080 70.0520 105.7080 90.0000 90.0000 90.0000
>> Data line--- SYMM 'C 2 2 21'
>>
>> Cell volume: 428071.531
>>
>> For estimated molecular weight 36000.
>> Nmol/asym Matthews Coeff %solvent P(2.30) P(tot)
>> _____________________________________________________________
>> 1 1.49 17.30 1.00 1.00
>> _____________________________________________________________
>>
>>
>> Space-Group Name: C 2 2 21
>> Space-Group Number: 20
>> Unit Cell: 57.81 70.05 105.71 90.00 90.00 90.00
>> MW of "average" protein to which Matthews applies: 36000
>> Resolution for Matthews calculation: 2.30
>>
>> Z MW VM % solvent rel. freq.
>> 1 36000 1.49 17.25 0.002 <== most probable
>>
>> Z is the number of multiples of the total composition
>> In most cases the most probable Z value should be 1
>> If it is not 1, you may need to consider other compositions
>>
>>
>> Histogram of relative frequencies of VM values
>> ----------------------------------------------
>> Frequency of most common VM value normalized to 1
>> VM values plotted in increments of 1/VM (0.02)
>>
>> <--- relative frequency --->
>> 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
>> | | | | | | | | | | |
>> 10.00 -
>> 8.33 -
>> 7.14 -
>> 6.25 -
>> 5.56 -
>> 5.00 -
>> 4.55 -
>> 4.17 --
>> 3.85 ---
>> 3.57 -----
>> 3.33 --------
>> 3.12 -------------
>> 2.94 -------------------
>> 2.78 ---------------------------
>> 2.63 ------------------------------------
>> 2.50 --------------------------------------------
>> 2.38 -------------------------------------------------
>> 2.27 --------------------------------------------------
>> 2.17 ---------------------------------------------
>> 2.08 -----------------------------------
>> 2.00 -----------------------
>> 1.92 -------------
>> 1.85 ------
>> 1.79 --
>> 1.72 -
>> 1.67 -
>> 1.61 -
>> 1.56 -
>> 1.52 -
>> 1.47 * (COMPOSITION*1)
>> 1.43 -
>> 1.39 -
>> 1.35 -
>> 1.32 -
>> 1.28 -
>> 1.25 -
>>
>>
>> Most probable VM for resolution = 2.30957
>> Most probable MW of protein in asu for resolution = 23168.4
>>
>>
>> Thanks in advance
>> Appu Kumar singh.
>
>
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