X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 277.15
Details 20mM Tris/HCl, pH=8.5, 50mM NaCl, 2mM DTT, 0.5mM PMSF

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.92 α = 90
b = 51.92 β = 90
c = 229.32 γ = 120
Symmetry
Space Group P 31 1 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2015-11-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA

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
2.03 76.44 97.4 0.032 -- -- 3.6 -- 23189 -- 0.0 --
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)
2.03 2.27 95.1 0.441 -- -- 3.6 --

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 2.03 45.0 -- -- -- 21335 1815 98.69 -- 0.22008 0.21688 0.26029 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 2.03 2.083 -- 151 1590 0.317 0.388 -- 99.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.938
Anisotropic B[1][1] 0.31
Anisotropic B[1][2] 0.15
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.99
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 5.716
r_mcbond_it 4.738
r_chiral_restr 0.072
r_bond_other_d 0.001
r_bond_refined_d 0.008
r_angle_other_deg 2.578
r_dihedral_angle_4_deg 16.173
r_angle_refined_deg 1.293
r_mcbond_other 4.737
r_scbond_other 5.811
r_long_range_B_other 8.241
r_scbond_it 5.814
r_gen_planes_refined 0.004
r_scangle_other 7.297
r_dihedral_angle_1_deg 5.226
r_mcangle_other 5.715
r_dihedral_angle_3_deg 12.265
r_long_range_B_refined 8.244
r_gen_planes_other 0.004
r_dihedral_angle_2_deg 34.207
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2329
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 57

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
REFMAC refinement version: 5.8.0049