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_gen_planes_other 0.003
r_gen_planes_refined 0.006
r_chiral_restr 0.074
r_dihedral_angle_4_deg 12.708
r_dihedral_angle_3_deg 15.117
r_dihedral_angle_2_deg 37.442
r_dihedral_angle_1_deg 5.813
r_angle_other_deg 0.954
r_angle_refined_deg 1.469
r_bond_other_d 0.004
r_bond_refined_d 0.011
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.5.1 molecular replacement
Xscale data reduction