X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details The reservoir solution contained 1-3% (w/v) polyethylene glycol 8000 (PEG 8000), 150 mM NaCl, and 8mM CaCl2.2H2O as precipitants in 10 mM Tris. The drops were prepared by mixing equivolume of virus solution (10mg/ml) in Tris-HCl Buffer (10 mM Tris-HCl, 150 mM NaCl, 8mM CaCl2.2H2O) with reservoir solution, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 255.4 α = 90
b = 350.4 β = 90.34
c = 271.6 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 mirror 2010-06-04
Diffraction Radiation
Monochromator Protocol
Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 0.9186 CHESS F1

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
2.7 50 93.1 -- 0.132 -- 2.6 1210268 1127217 0.0 0.0 --
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)
2.7 2.8 94.7 -- 0.378 2.4 2.4 --

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
-- 2.7 50.0 -- 0.0 -- -- 56289 86.7 -- -- 0.216 0.2169 --
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 2.7 2.8 -- 5282 98565 0.31 0.3111 -- 80.0
X Ray Diffraction 2.8 2.91 -- 5453 101647 0.2918 0.2897 -- 82.5
X Ray Diffraction 2.91 3.04 -- 5444 104633 0.2751 0.2754 -- 84.7
X Ray Diffraction 3.04 3.2 -- 5696 106124 0.2593 0.2621 -- 86.2
X Ray Diffraction 3.2 3.4 -- 5762 108528 0.2373 0.2387 -- 87.9
X Ray Diffraction 3.4 3.66 -- 5688 110042 0.223 0.2256 -- 89.1
X Ray Diffraction 3.66 4.03 -- 5750 110445 0.2059 0.2054 -- 89.4
X Ray Diffraction 4.03 4.62 -- 5777 112038 0.1706 0.17 -- 90.6
X Ray Diffraction 4.62 5.81 -- 5859 110819 0.169 0.1678 -- 89.6
X Ray Diffraction 5.81 50.0 -- 5578 108087 0.1893 0.1916 -- 86.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.126
Anisotropic B[1][1] -3.118
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.62
Anisotropic B[2][2] 1.979
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.139
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.164
c_mcangle_it 1.991
c_scbond_it 2.036
c_mcbond_it 1.141
c_angle_d 1.365
c_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4375
Nucleic Acid Atoms 194
Heterogen Atoms 40
Solvent Atoms 131

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMoRE Structure Solution
CNS 1.3 Structure Refinement
Software
Software Name Purpose
CNS version: 1.3 refinement
AMoRE model building
HKL-2000 data collection