X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 277.15
Details 18% PEG 1000, 17% glycerol, 0.1M HEPES pH 7.0 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution), VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.1 α = 90
b = 96.42 β = 90
c = 57.71 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2011-09-23
Diffraction Radiation
Monochromator Protocol
Flat graphite crystal 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
2 29.51 100.0 0.088 -- -- 5.0 15860 15847 0.0 0.0 33.5
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)
2.0 2.11 100.0 0.673 -- 2.2 5.0 2283

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 2.0 27.48 2.0 0.0 15847 15057 790 99.95 -- 0.21126 0.20953 0.2455 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 2.0 2.052 -- 56 1103 0.273 0.3 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.986
Anisotropic B[1][1] 1.88
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.06
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.009
r_chiral_restr 0.091
r_dihedral_angle_4_deg 18.697
r_dihedral_angle_3_deg 13.311
r_dihedral_angle_2_deg 33.492
r_dihedral_angle_1_deg 6.262
r_angle_other_deg 0.785
r_angle_refined_deg 1.593
r_bond_other_d 0.001
r_bond_refined_d 0.016
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 937
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 146

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0032 refinement
PHASER model building
CrystalClear data collection