X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 277.0
Details 5.00% Glycerol, 19.00% iso-Propanol, 19.00% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.89 α = 90
b = 77.89 β = 90
c = 64.09 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2012-02-09
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97975,0.91162,0.97916 SSRL BL11-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.8 29.85 99.4 0.104 -- -- -- -- 21120 -- -3.0 17.128
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.8 1.86 97.6 0.578 -- 2.0 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MAD 1.8 29.847 -- 0.0 -- 21100 1086 99.63 -- 0.1496 0.1474 0.1901 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.801 1.847 -- 66 1447 0.245 0.27 -- 98.57
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.6735
Anisotropic B[1][1] 0.3
Anisotropic B[1][2] 0.15
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.3
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.45
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.013
r_chiral_restr 0.09
r_mcangle_it 2.307
r_bond_other_d 0.001
r_dihedral_angle_1_deg 5.795
r_mcbond_it 1.424
r_angle_other_deg 0.91
r_gen_planes_other 0.001
r_dihedral_angle_3_deg 10.956
r_dihedral_angle_4_deg 18.907
r_dihedral_angle_2_deg 33.197
r_mcbond_other 0.42
r_scbond_it 3.859
r_gen_planes_refined 0.006
r_scangle_it 5.668
r_angle_refined_deg 1.315
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1594
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 319

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling version: December 29, 2011
REFMAC refinement version: 5.5.0110
XDS data reduction
SHELXD phasing