X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 293.15
Details 25% medium molecular weight PEG smears, 0.1M citrate, pH 5.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.35 α = 90
b = 48.35 β = 90
c = 137.41 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2018-07-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.0000 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
2.3 45.8 100.0 0.057 -- -- 5.6 -- 7846 -- -- 35.4
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)
2.3 2.38 100.0 0.169 -- -- 5.8 --

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 2.3 45.61 -- -- -- 7398 390 99.85 -- 0.21372 0.21137 0.26086 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 2.3 2.36 -- 24 517 0.201 0.39 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.457
Anisotropic B[1][1] -1.42
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.83
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.059
r_gen_planes_other 0.003
r_dihedral_angle_4_deg 18.291
r_long_range_B_refined 5.638
r_scangle_other 3.292
r_dihedral_angle_1_deg 8.465
r_angle_other_deg 1.112
r_bond_other_d 0.001
r_mcbond_other 1.618
r_scbond_other 2.044
r_mcbond_it 1.633
r_mcangle_it 2.665
r_scbond_it 2.046
r_dihedral_angle_2_deg 23.664
r_mcangle_other 2.663
r_angle_refined_deg 1.261
r_long_range_B_other 5.641
r_bond_refined_d 0.013
r_dihedral_angle_3_deg 13.636
r_gen_planes_refined 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1178
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 29

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0232
XDS data reduction
Aimless data scaling
PHASER phasing