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CCP4BB  June 2015

CCP4BB June 2015

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Subject:

Re: crystal habit/morphology and the relationship to unit cell contents

From:

Paul Paukstelis <[log in to unmask]>

Reply-To:

Paul Paukstelis <[log in to unmask]>

Date:

Mon, 1 Jun 2015 16:41:41 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (115 lines)

All the crystals are unipyramidal, regardless of how they are grown. The 
crystal habit seems to be dictated by the arrangement of the molecules 
in the unit cell. The structure is solved, so this is really an exercise 
in trying to figure out if what we see in the crystal packing can 
explain the morphology.

--paul

On 06/01/2015 04:25 PM, Edward A. Berry wrote:
> Is it possible to distinguish P64 from P62 without having basically 
> solved the structure?
>
> Given that it is P64,  is the +ive direction of the c axis arbitrary? 
> A left-hand helix is left hand either way you point it, and the 
> molecules in the asymmetric units could be pointing the opposite way.
> Clearly the lattice is symmetric, so you could start out with either 
> orientation and end up solving the structure. Phaser offers to try 
> both enantiomers, but not to try with rotating the lattice to reverse 
> the c axis in case you got that wrong.
>
> I too would first guess that the truncated base is where it ran into 
> the glass, and the flat tip
> may be where it hit the air-water interface; the basic morphology 
> being hexagonal bipyramid.
> Unless there are dozens of crystals with the same habit.
>
> eab
>
> On 06/01/2015 03:45 PM, Roberts, Sue A - (suer) wrote:
>> Can't you break the ambiguity if there is significant anomalous 
>> signal? So, you'd need to have collected data from a protein crystal 
>> with SeMet, or a heavy atom, or near the S edge, and know the 
>> orientation of the crystal w.r.t. the direction of the unique crystal 
>> axis (for instance from face indexing.)
>>
>> Sue
>>
>> Dr. Sue A. Roberts
>> Dept. of Chemistry and Biochemistry
>> University of Arizona
>> 1306 E. University Blvd,  Tucson, AZ 85721
>> Phone: 520 621 4168
>> [log in to unmask]
>>
>>
>> -----Original Message-----
>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of 
>> Phil Jeffrey
>> Sent: Monday, June 01, 2015 12:24 PM
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] crystal habit/morphology and the relationship 
>> to unit cell contents
>>
>> I would have thought that what the indexing routine defined as [001] 
>> vs [00-1] would be essentially random as one would obtain the 
>> equivalent indexing in 622 in both "up" and "down" alignment of the 
>> crystallographic a/b/c axes with respect to crystal morphology.
>>
>> Phil Jeffrey
>> Princeton
>>
>>
>>
>> On 6/1/15 1:44 PM, Scott Lovell wrote:
>>> Hi Paul,
>>>
>>> If you have access to diffractometer equipped with a 4-circle 
>>> goniometer, you should be able to index the faces of the crystals.  
>>> All you need to do is collect some images to index the lattice and 
>>> determine the orientation matrix.  Most instruments have software 
>>> that allows one to then orient specific faces or crystallographic 
>>> directions relative to various directions of the instrument (eg. 
>>> camera, phi axis, direct beam, etc).  So after indexing, you could 
>>> then orient the [001] direction of the crystal towards the camera to 
>>> determine if this is the "top" or the "base".  You can also 
>>> determine the direction of the a/b axes [100] and [010] relative to 
>>> the crystal and index the other faces.  If you can also measure the 
>>> interfacial angles, this may help you to confirm the indices.
>>>
>>> If you do this for a number of samples, is the "top" face always the 
>>> [001] direction or is it the [00-1] direction for other crystals?  
>>> Assuming that you are growing these crystals by hanging drop, my 
>>> guess is that the "base" is in contact with the coverslip during 
>>> growth and you observe this half pyramid habit.  If you were to grow 
>>> the crystals using the floating drop method, to prevent contact with 
>>> the plate materials, would the crystals form a bipyramidal habit?  
>>> Or do you see crystals in the current drop that have the same habit 
>>> but are not in contact with the plate materials?
>>>
>>> Scott
>>>
>>>
>>> -----Original Message-----
>>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
>>> Paul Paukstelis
>>> Sent: Monday, June 01, 2015 11:21 AM
>>> To: [log in to unmask]
>>> Subject: [ccp4bb] crystal habit/morphology and the relationship to
>>> unit cell contents
>>>
>>> I'm interested in knowing how to figure out the relationship between 
>>> the unit cell contents and the crystal habit in these crystals 
>>> (small attachment, two roughly orthogonal views).
>>>
>>> Space group is P64 (enantiomeric) , and you can clearly see the 
>>> six-fold. The question becomes how to determine which direction the 
>>> screw axis is going with respect to "top" and the "base" of the 
>>> pyramidal crystals (right image) so I can gauge how/why the crystals 
>>> grow this way based on the cell contents.
>>>
>>> Thanks in advance.
>>>
>>> --paul
>>>

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