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 50 mM

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.37 α = 90
b = 41.44 β = 104.45
c = 72.22 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
PIXEL DECTRIS PILATUS 6M-F -- 2015-07-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1

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
1.05 41.44 97.1 0.061 -- -- 4.75 -- 109788 -- -3.0 12.331
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)
1.05 1.11 86.1 0.579 -- 2.07 3.77 --

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 1.05 30.0 -- 0.0 -- 104237 5512 97.18 -- 0.1343 0.1335 0.1485 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 1.051 1.078 -- 328 6075 0.296 0.289 -- 76.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.319
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 0.788
r_dihedral_angle_1_deg 6.31
r_sphericity_bonded 6.501
r_sphericity_free 25.66
r_dihedral_angle_4_deg 21.09
r_mcangle_it 0.908
r_mcbond_other 0.63
r_dihedral_angle_2_deg 34.995
r_bond_other_d 0.001
r_angle_refined_deg 1.176
r_gen_planes_refined 0.005
r_angle_other_deg 0.719
r_gen_planes_other 0.001
r_bond_refined_d 0.005
r_chiral_restr 0.074
r_mcbond_it 0.64
r_dihedral_angle_3_deg 10.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2047
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 418

Software

Software
Software Name Purpose
XSCALE data scaling
REFMAC refinement version: 5.8.0073
PDB_EXTRACT data extraction version: 3.20
XDS data reduction
REFMAC phasing