X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 289.0
Details ButhA.00063.a.A1 PS01164 at 31 mg/mL with 5 mM L-histidine against Wizard III A3 focus screen, 350 mM magnesium formate, 12% PEG 3350 with 20% glycerol as cryo-protectant, crystal tracking ID 230808g3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.16 α = 90
b = 116.36 β = 90
c = 142.99 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
CCD ADSC QUANTUM 315r -- 2012-02-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.3 0.976484 ALS 5.0.3

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
2.65 50 99.5 0.065 -- -- 7.8 34582 34582 -- -3.0 56.022
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)
2.65 2.72 99.9 0.524 -- 4.22 -- --

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 2.65 19.61 -- 0.0 -- 34582 1742 99.46 -- 0.2078 0.206 0.2404 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 2.65 2.719 -- 129 2212 0.33 0.407 -- 99.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 51.8046
Anisotropic B[1][1] -3.91
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.87
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.374
r_dihedral_angle_4_deg 25.247
r_gen_planes_refined 0.007
r_angle_other_deg 1.13
r_bond_other_d 0.004
r_gen_planes_other 0.004
r_angle_refined_deg 1.464
r_chiral_restr 0.075
r_bond_refined_d 0.012
r_dihedral_angle_3_deg 15.453
r_dihedral_angle_2_deg 33.258
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6041
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 64

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.3.0
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
XDS data reduction