X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 298.0
Details 0.1 M Bis-tris pH 5.0, 13% PEG 3350, 0.2 M NaHCOO, 22 mg/ml protein

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 123.86 α = 90
b = 126.96 β = 90
c = 62.57 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2016-06-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2

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
1.7 40 99.8 -- -- -- 13.4 -- 108841 -- -- --
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)
1.7 1.73 100.0 -- -- 1.3 13.8 --

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 1.7 40.0 -- -- -- 103324 5400 99.63 -- 0.19094 0.18919 0.22324 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 1.7 1.744 -- 405 7555 0.344 0.331 -- 99.59
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.19
Anisotropic B[1][1] 0.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.42
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_other 4.494
r_scbond_it 3.167
r_dihedral_angle_4_deg 18.734
r_bond_other_d 0.001
r_dihedral_angle_2_deg 35.919
r_gen_planes_other 0.005
r_mcangle_other 3.279
r_mcbond_other 2.515
r_mcbond_it 2.515
r_long_range_B_refined 6.3
r_angle_refined_deg 1.437
r_mcangle_it 3.279
r_angle_other_deg 0.778
r_long_range_B_other 6.276
r_dihedral_angle_3_deg 13.8
r_scbond_other 3.166
r_bond_refined_d 0.012
r_gen_planes_refined 0.016
r_dihedral_angle_1_deg 6.617
r_chiral_restr 0.114
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7152
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 377

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
XDS data reduction
Aimless data scaling
PHASER phasing