X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 277.0
Details 0.2000M Li2SO4, 10.0000% PEG-3000, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.63 α = 90
b = 93.48 β = 95.29
c = 98.8 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-07-31
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97922 SSRL BL9-2

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
1.9 29.49 98.0 0.069 -- -- -- -- 105637 -- -3.0 25.053
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)
1.9 1.97 95.8 0.554 -- 1.5 -- --

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 1.9 29.488 -- 0.0 -- 105611 5276 99.34 -- 0.187 0.185 0.221 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 1.9 1.95 -- 368 7193 0.245 0.283 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.272
Anisotropic B[1][1] -1.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.1
Anisotropic B[2][2] 0.88
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.11
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.781
r_mcbond_other 0.29
r_dihedral_angle_3_deg 10.341
r_mcbond_it 1.056
r_bond_other_d 0.002
r_scbond_it 3.038
r_scangle_it 4.529
r_gen_planes_refined 0.007
r_mcangle_it 1.923
r_bond_refined_d 0.016
r_dihedral_angle_2_deg 29.863
r_dihedral_angle_4_deg 12.381
r_angle_refined_deg 1.31
r_dihedral_angle_1_deg 4.254
r_chiral_restr 0.069
r_gen_planes_other 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8875
Nucleic Acid Atoms 0
Heterogen Atoms 206
Solvent Atoms 869

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PHENIX refinement
SHELX phasing
REFMAC refinement version: 5.5.0102
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.006
XDS data reduction
SHELXD phasing
autoSHARP phasing