X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 1.6 M sodium nitrate, 0.16 M calcium chloride, 0.2 M bis-tris pH 6.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.72 α = 90
b = 67.72 β = 90
c = 107.32 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 9M -- 2017-06-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97908 NSLS-II 17-ID-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
1.71 57.27 99.75 -- -- -- 12.9 -- 26111 -- -- --
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)
-- -- -- -- -- -- -- --

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 1.71 57.27 -- -- -- 26111 1356 99.75 -- 0.15268 0.15158 0.17332 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 1.714 1.758 -- 89 1832 0.349 0.343 -- 97.02
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.469
Anisotropic B[1][1] -0.28
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.28
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.56
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.01
r_gen_planes_refined 0.012
r_bond_refined_d 0.024
r_angle_refined_deg 2.102
r_scbond_it 2.284
r_long_range_B_other 5.533
r_dihedral_angle_3_deg 12.873
r_dihedral_angle_4_deg 21.62
r_long_range_B_refined 6.581
r_mcangle_other 1.664
r_mcbond_it 1.243
r_gen_planes_other 0.002
r_mcangle_it 1.663
r_chiral_restr 0.132
r_scangle_other 3.303
r_bond_other_d 0.002
r_mcbond_other 1.24
r_scbond_other 2.283
r_dihedral_angle_2_deg 36.836
r_dihedral_angle_1_deg 6.551
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2032
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 427

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0073
XDS data reduction
XDS data scaling
MOLREP phasing