X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.0
Details 0.2M NaI, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.6 α = 90
b = 42.86 β = 90
c = 79.43 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2012-06-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418 -- --

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
1.72 19.45 99.5 0.119 0.119 -- 4.6 14573 14500 -- -- 15.3
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)
1.72 1.81 99.0 0.766 0.766 1.0 4.5 2056

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 1.72 19.45 -- 0.0 14576 14452 727 99.15 0.1596 0.1596 0.1564 0.2201 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 1.72 1.764 -- 53 885 0.267 0.328 -- 98.74
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.931
Anisotropic B[1][1] 0.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 12.177
r_angle_refined_deg 1.561
r_dihedral_angle_4_deg 18.725
r_bond_refined_d 0.015
r_dihedral_angle_1_deg 5.337
r_gen_planes_other 0.001
r_sphericity_bonded 16.762
r_gen_planes_refined 0.009
r_bond_other_d 0.001
r_angle_other_deg 0.952
r_dihedral_angle_2_deg 37.379
r_chiral_restr 0.086
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1052
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 188

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.20
PHASER phasing version: 2.3.0
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
CrystalClear data collection
XDS data reduction