X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9.5
Temperature 277.0
Details 0.2 M NaCl, 0.1 M CHES, 1.26 M (NH4)2SO4, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.15 α = 90
b = 104.98 β = 90
c = 123.25 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r mirrors 2013-07-08
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.97933 APS 19-BM

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
2.01 30 99.8 0.098 -- -- 5.8 45198 45121 -- -3.0 32.36
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)
2.01 2.04 100.0 0.897 -- 1.72 4.9 2244

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
SAD 2.01 29.06 -- 0.0 45109 45109 1160 99.78 0.1849 0.1849 0.1839 0.2272 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 2.01 2.06 3257 79 3178 0.1936 0.2648 -- 99.78
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 39.4646
Anisotropic B[1][1] 0.38
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.6108
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.2308
RMS Deviations
Key Refinement Restraint Deviation
t_angle_deg 1.08
t_omega_torsion 3.7
t_other_torsion 2.74
t_bond_d 0.013
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.284
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5163
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 202

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
BUSTER-TNT refinement version: BUSTER 2.10.0
PDB_EXTRACT data extraction version: 3.11
SBC-Collect data collection
SHELX phasing
MLPHARE phasing
DM phasing
BUCCANEER phasing
Coot model building
BUSTER refinement version: 2.10.0