X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 298.0
Details 0.2 M ammonium phosphate, 0.1 M Tris:HCl, pH 8.5, 50% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.82 α = 90
b = 117.9 β = 90
c = 166.32 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2012-08-15
Diffraction Radiation
Monochromator Protocol
-- SAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID -- APS 31-ID

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
2.8 50 98.2 0.092 -- -- 3.0 -- 108628 -- -- --
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)
2.8 2.85 99.7 0.966 -- -- 3.0 5454

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 2.8 19.9 -- 0.0 -- 56804 2883 98.37 -- 0.1939 0.1925 0.2195 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 2.8 2.871 -- 211 3965 0.322 0.351 -- 99.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 95.6415
Anisotropic B[1][1] 0.21
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.22
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.009
r_chiral_restr 0.091
r_dihedral_angle_4_deg 19.744
r_dihedral_angle_3_deg 15.787
r_dihedral_angle_2_deg 35.328
r_dihedral_angle_1_deg 5.974
r_angle_refined_deg 1.757
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13981
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 79

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-3000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
phenix Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
SCALEPACK data reduction