X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 293.0
Details 0.1M HEPES pH 7.5, 20% PEG 8000, vapor diffusion, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.12 α = 90
b = 62.4 β = 90
c = 66.06 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U

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
1.6 45.36 99.7 -- 0.123 -- 4.2 22474 22474 -- -- --
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)
1.6 1.69 99.8 0.521 0.521 1.4 4.2 3254

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
MOLECULAR REPLACEMENT 1.6 34.29 -- 0.0 -- 22322 1142 99.03 -- 0.1885 0.186 0.2374 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 1.6 1.641 -- 66 1425 0.276 0.332 -- 99.67
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.3801
Anisotropic B[1][1] -0.35
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.41
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.009
r_chiral_restr 0.112
r_dihedral_angle_4_deg 15.037
r_dihedral_angle_3_deg 15.095
r_dihedral_angle_2_deg 31.183
r_dihedral_angle_1_deg 5.835
r_angle_other_deg 0.965
r_angle_refined_deg 1.751
r_bond_other_d 0.001
r_bond_refined_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1214
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 158

Software

Computing
Computing Package Purpose
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
MOLREP molecular replacement
SCALA version: 3.3.20 data reduction