X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.25
Temperature 277.15
Details 32% Low Molecular-Weight PEG Smears, 0.1M MES pH 6.25 (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 = 82.7 α = 90
b = 96.46 β = 90
c = 57.74 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 -- 2011-10-03
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
2.05 19.68 99.8 0.12 -- -- 5.0 14789 14774 0.0 0.0 30.8
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)
2.05 2.16 99.8 0.791 -- 2.0 5.1 2097

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 2.05 19.6 2.0 0.0 14774 14026 747 99.56 -- 0.18582 0.18376 0.2276 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 2.05 2.103 -- 61 981 0.314 0.306 -- 99.33
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.822
Anisotropic B[1][1] 4.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.69
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.015
r_dihedral_angle_4_deg 14.07
r_angle_refined_deg 1.577
r_dihedral_angle_1_deg 5.764
r_gen_planes_other 0.002
r_gen_planes_refined 0.008
r_dihedral_angle_3_deg 12.742
r_dihedral_angle_2_deg 31.876
r_chiral_restr 0.091
r_angle_other_deg 0.882
r_bond_other_d 0.002
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.273
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 937
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 169

Software

Software
Software Name Purpose
CrystalClear data collection
PHASER phasing
REFMAC refinement version: 5.7.0032
XDS data reduction
SCALA data scaling