X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8
Temperature 296.0
Details 1.5 M sodium citrate, Tris 50mM , pH 8.0, VAPOR DIFFUSION, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.24 α = 90
b = 41.21 β = 104.21
c = 71.99 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 OXFORD ONYX CCD -- 2013-04-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.542 -- --

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
1.5 89.16 89.1 0.037 -- -- -- -- 34424 -- -3.0 15.767
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)
1.5 1.59 74.3 0.323 -- 2.98 -- --

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 1.55 29.07 -- 0.0 -- 31909 1632 90.8 -- 0.1621 0.1609 0.1856 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 1.55 1.59 -- 109 1851 0.211 0.243 -- 76.09
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.8539
Anisotropic B[1][1] 0.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.09
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_chiral_restr 0.071
r_mcbond_other 0.433
r_bond_refined_d 0.007
r_dihedral_angle_4_deg 25.071
r_dihedral_angle_1_deg 6.179
r_mcangle_it 0.793
r_mcbond_it 0.438
r_bond_other_d 0.002
r_dihedral_angle_3_deg 12.849
r_gen_planes_refined 0.004
r_angle_other_deg 0.793
r_angle_refined_deg 1.283
r_dihedral_angle_2_deg 35.616
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2038
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 303

Software

Software
Software Name Purpose
XSCALE data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
XDS data reduction
XDS data scaling