X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 291.0
Details 0.1 M Sodium Cacodylate, pH 6, 15% PEG 8000, 15% Glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.27 α = 91.37
b = 49.13 β = 93.57
c = 107.46 γ = 95.75
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M mirrors 2012-06-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03

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
2.09 48.86 97.5 0.098 -- -- 2.0 -- 54249 -- -- --
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)
2.09 2.14 95.7 0.358 -- 2.0 2.0 3935

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 2.09 48.86 -- 0.0 -- 54207 2757 97.48 -- 0.1783 0.1756 0.2263 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 2.09 2.144 -- 194 3730 0.226 0.268 -- 95.66
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 51.539
Anisotropic B[1][1] 0.13
Anisotropic B[1][2] 0.2
Anisotropic B[1][3] -0.05
Anisotropic B[2][2] -0.95
Anisotropic B[2][3] 0.52
Anisotropic B[3][3] 0.76
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.041
r_bond_refined_d 0.017
r_mcbond_it 1.238
r_dihedral_angle_1_deg 7.254
r_dihedral_angle_3_deg 16.547
r_bond_other_d 0.002
r_dihedral_angle_4_deg 17.379
r_gen_planes_refined 0.009
r_dihedral_angle_2_deg 33.367
r_angle_refined_deg 1.857
r_chiral_restr 0.11
r_gen_planes_other 0.001
r_angle_other_deg 0.92
r_mcbond_other 1.238
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6366
Nucleic Acid Atoms 0
Heterogen Atoms 77
Solvent Atoms 497

Software

Software
Software Name Purpose
XDS data reduction version: 0.1.16
Aimless data scaling version: 2.5.5
PDB_EXTRACT data extraction version: 3.14
PHASER phasing
REFMAC refinement version: 5.8.0049
GDA data reduction