X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 295.0
Details 0.1 M sodium acetate pH 4.5, 30% w/V PEG 8000, 0.2M lithium sulfate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.64 α = 90
b = 66.64 β = 90
c = 82.18 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2016-05-18
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal monochromator, non fixed exit slit SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97 SSRL BL9-2

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
2.18 50 99.4 0.07 -- -- 5.4 -- 18619 -- -- --
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)
2.18 2.22 97.9 0.493 -- -- 4.7 --

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 47.12 -- 0.0 -- 15201 800 99.95 -- 0.1988 0.1972 0.2279 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 -- 71 1087 0.115 0.186 0.0 99.91
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 51.935
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 26.076
r_chiral_restr 0.061
r_gen_planes_other 0.001
r_bond_refined_d 0.006
r_bond_other_d 0.001
r_dihedral_angle_1_deg 5.837
r_angle_refined_deg 1.1
r_dihedral_angle_4_deg 11.953
r_gen_planes_refined 0.003
r_angle_other_deg 0.82
r_dihedral_angle_3_deg 12.033
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1577
Nucleic Acid Atoms 0
Heterogen Atoms 101
Solvent Atoms 115

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.22
HKL-2000 data reduction
REFMAC phasing