X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details BuviA.00139.a.B1 PS01581 at 26.1 mg/mL against MCSG 1 screen condition G5, 2 M ammonium sulfate, 0.1 M BisTris pH 6.5, with 20% ethylene glycol as cryo-protectant, crystal tracking ID 236782g5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.42 α = 90
b = 116.42 β = 90
c = 89.97 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ VariMax 2012-08-28
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
2.05 50 99.3 0.073 -- -- 10.3 44492 44198 -- -3.0 34.916
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 2.1 97.6 0.417 -- 4.57 -- --

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 44.02 -- 0.0 -- 44196 2234 99.33 -- 0.2028 0.2012 0.2338 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 -- 156 3033 0.227 0.26 -- 97.46
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.514
Anisotropic B[1][1] 0.22
Anisotropic B[1][2] 0.22
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.71
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.81
r_bond_other_d 0.001
r_gen_planes_other 0.001
r_angle_refined_deg 1.46
r_gen_planes_refined 0.007
r_chiral_restr 0.085
r_dihedral_angle_1_deg 5.761
r_dihedral_angle_2_deg 35.287
r_dihedral_angle_4_deg 19.725
r_bond_refined_d 0.013
r_dihedral_angle_3_deg 14.206
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3052
Nucleic Acid Atoms 0
Heterogen Atoms 55
Solvent Atoms 296

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.5.1
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
StructureStudio data collection
XDS data reduction