X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 293.0
Details 20 mM MgAC2, 13% MPD, 0.1 M MES

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 133.99 α = 90
b = 299.3 β = 112.24
c = 143.47 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 EIGER X 16M -- 2016-11-16
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
3 50 98.9 0.091 -- -- 3.1 -- 206139 -- -- --
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)
3.0 3.1 99.6 0.559 -- -- -- --

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 3.0 15.0 -- -- -- 194272 10224 98.26 -- 0.17941 0.17796 0.20686 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 3.0 3.075 -- 735 13972 0.336 0.352 -- 99.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 78.177
Anisotropic B[1][1] 2.88
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.53
Anisotropic B[2][2] -5.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.78
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_rigid_bond_restr 1.233
r_dihedral_angle_3_deg 15.034
r_mcbond_other 2.631
r_long_range_B_refined 4.092
r_dihedral_angle_2_deg 35.099
r_angle_other_deg 0.916
r_mcangle_other 3.52
r_sphericity_free 35.924
r_dihedral_angle_4_deg 14.692
r_scangle_other 3.056
r_angle_refined_deg 1.207
r_chiral_restr 0.071
r_long_range_B_other 4.063
r_bond_other_d 0.002
r_sphericity_bonded 6.912
r_mcangle_it 3.52
r_dihedral_angle_1_deg 5.978
r_scbond_it 2.498
r_mcbond_it 2.631
r_bond_refined_d 0.007
r_scbond_other 2.496
r_gen_planes_refined 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 48944
Nucleic Acid Atoms 0
Heterogen Atoms 180
Solvent Atoms 269

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
REFMAC phasing
REFMAC refinement version: 5.8.0158