X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 298.0
Details 0.1 M CdCl, 0.1 M Acetate pH 4.5, 32% PEG 400

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.62 α = 90
b = 59.62 β = 90
c = 110.05 γ = 90
Symmetry
Space Group P 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2018-07-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1

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
1.87 40.44 99.4 0.106 -- -- 12.7 -- 17026 -- -- --
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)
1.87 1.92 99.0 2.796 -- -- 13.1 1218

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
FOURIER SYNTHESIS 1.87 40.47 -- 0.0 -- 16169 816 99.33 -- 0.2119 0.2092 0.2724 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 1.87 1.919 -- 58 1156 0.367 0.384 -- 98.86
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.609
Anisotropic B[1][1] 2.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.37
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 12.493
r_gen_planes_refined 0.007
r_mcbond_other 3.899
r_gen_planes_other 0.001
r_bond_refined_d 0.007
r_dihedral_angle_2_deg 29.807
r_bond_other_d 0.001
r_dihedral_angle_3_deg 17.321
r_dihedral_angle_1_deg 7.453
r_angle_other_deg 1.275
r_chiral_restr 0.068
r_angle_refined_deg 1.444
r_mcangle_it 5.964
r_mcbond_it 3.921
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1369
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 72

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0238
Aimless data scaling version: 0.7.1
PDB_EXTRACT data extraction version: 3.23
XDS data reduction
REFMAC phasing