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 with 2 mM ADP against Morpheus screen condition F1, 10% PEG 20,000, 20% PEG 550 MME, 0.02 M each monosaccharide, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 237917f1, unique puck ID beh5-16, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 115.86 α = 90
b = 115.86 β = 90
c = 91.64 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 ADSC QUANTUM 315r -- 2012-10-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1

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
2.6 50 99.7 0.046 -- -- 5.2 22230 22169 -- -3.0 59.114
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)
2.6 2.67 99.8 0.5 -- 3.7 -- --

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 2.6 44.04 -- 0.0 -- 22169 1130 99.73 -- 0.2148 0.2128 0.2518 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 2.6 2.667 -- 76 1538 0.332 0.39 -- 99.81
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.8381
Anisotropic B[1][1] 0.69
Anisotropic B[1][2] 0.69
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.69
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.24
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.011
r_angle_refined_deg 1.469
r_dihedral_angle_4_deg 12.708
r_dihedral_angle_1_deg 5.813
r_dihedral_angle_3_deg 15.117
r_gen_planes_refined 0.006
r_bond_other_d 0.004
r_gen_planes_other 0.003
r_chiral_restr 0.074
r_angle_other_deg 0.954
r_dihedral_angle_2_deg 37.442
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2963
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 53

Software

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