Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.9 Å3/Da / Density % sol: 68.4 % Description: 3 DIFFERENT CRYSTAL FORMS WERE AVAILABLE - P41211, P21212 AND P3121. THIS CRYSTAL IS THE ONLY ONE FOR THE FORM P3121 AND WAS PREPARED AS OS-DERIVATIVE. THE STRUCTURE WAS SOLVED BY SIRAS ...Description: 3 DIFFERENT CRYSTAL FORMS WERE AVAILABLE - P41211, P21212 AND P3121. THIS CRYSTAL IS THE ONLY ONE FOR THE FORM P3121 AND WAS PREPARED AS OS-DERIVATIVE. THE STRUCTURE WAS SOLVED BY SIRAS USING NATIVE AND AU- DERIVATIVE DATA OF ANISOTROPIC CRYSTAL FORM P41211. THIS INITIAL PHASES WERE USED AS STARTING POINT FOR DMMULTI. THE BEST ELECTRON DENSITY MAP WAS OBTAINED FROM THE DATA FROM P3121 CRYSTAL. THIS WAS ALSO THE ONLY FORM WHERE DOMAIN 9 WAS NICELY ORDERED AND THE SEQUENCE COULD BE PLACED IN THE ELECTRON DENSITY. 2 OS ATOMS THAT ARE PRESENT IN THE STRUCTURE SHOULD COME FROM THE SOAKING. NEVERTHELESS, THE STRUCTURE COULD NOT BE SOLVED BY SAD USING ONLY THIS DATA. CA ATOM PRESENT IN DOMAIN 7 IS ALSO PRESENT IN NATIVE STRUCTURES FROM OTHER FORMS. TWO OTHER FORMS WERE NOT FURTHER REFINED AND DEPOSITED WHILE DOMAIN 9 IS PARTIALLY DISORDERED.
Crystal grow
Details: CA. 5MG/ML PROTEIN CONC. 2-2.4M SODIUM MALONATE PH 7.0
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9486 Å / Relative weight: 1
Reflection
Resolution: 3.1→20 Å / Num. obs: 9719 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.2
Reflection shell
Resolution: 3.1→3.15 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 83.6
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Processing
Software
Name
Version
Classification
DENZO
datareduction
SCALEPACK
datascaling
PHENIX
phasing
DM
phasing
REFMAC
5.8.0107
refinement
Refinement
Method to determine structure: SIRAS Starting model: NONE Resolution: 3.1→19.75 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.831 / SU B: 20.708 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 3 DIFFERENT CRYSTAL FORMS WERE AVAILABLE - P41211, P21212 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 3 DIFFERENT CRYSTAL FORMS WERE AVAILABLE - P41211, P21212 AND P3121. THIS CRYSTAL IS THE ONLY ONE FOR THE FORM P3121. ONLY IN THIS FORM DOMAIN 9 WAS NICELY ORDERED AND THE SEQUENCE COULD BE PLACED IN ELECTRON DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2897
487
4.9 %
RANDOM
Rwork
0.21638
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obs
0.21993
9372
92.49 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK