X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 289.0
Details ButhA.00092.a.B1 PS01671 at 23.6 mg/mL against MCSG1 screen condition d3, 0.2 M MgCl2, 0.1 M TrisHCl pH 8.5, 30% PEG 400, crystal tracking ID 240482d3, unique puck ID quk9-15, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 141.6 α = 90
b = 60.1 β = 112.86
c = 103.19 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2013-01-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.283574 SSRL BL7-1

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
1.75 50 98.8 0.037 -- -- -- -- 79884 -- -3.0 29.078
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)
1.75 1.8 95.8 0.26 -- 4.64 -- --

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 1.75 19.63 -- 0.0 -- 79883 4014 98.87 -- 0.1693 0.1676 0.201 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 1.75 1.795 -- 256 5418 0.217 0.25 -- 95.78
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.4711
Anisotropic B[1][1] 0.92
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.36
Anisotropic B[2][2] 0.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.551
r_mcbond_other 1.02
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_angle_refined_deg 1.408
r_angle_other_deg 0.807
r_dihedral_angle_1_deg 5.656
r_dihedral_angle_2_deg 35.413
r_dihedral_angle_3_deg 12.157
r_dihedral_angle_4_deg 16.973
r_chiral_restr 0.085
r_gen_planes_refined 0.007
r_gen_planes_other 0.001
r_mcbond_it 1.023
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5339
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 799

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.5.2 molecular replacement
Xscale data reduction