X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 285.0
Details 1 microliter of VP1 at 10 mg/ml in 25 mM Na-HEPES, pH 7.8, 100 mM NaCl mixed with 2 microliter of crystallization buffer [25 mM Na-MES, pH 6.5, 1.5% (w/v) PEG 3350] and allowing the drop to equilibrate at 12 C by hanging-drop vapor diffusion with a well solution identical in composition to the drop except for the protein. With micro-seeding, thin, plate-like crystals appeared after 1 day and grew to full size in about two weeks., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.35 α = 90
b = 112.75 β = 90
c = 143.79 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 315 Superbend (5.0 T, single pole) 2004-04-10
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 1.000 ALS 8.2.1

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 90.1 0.073 -- -- 3.5 -- 35449 -- -- --
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 2.69 45.1 0.397 -- -- 1.6 1753

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
MIRAS 2.6 50.0 -- 0.0 -- 32893 2620 84.5 -- -- 0.241 0.29 RANDOM
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.906
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.009
c_angle_d 1.294
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8699
Nucleic Acid Atoms 145
Heterogen Atoms 32
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHARP phasing
DM phasing version: 4.2
CNS refinement
PDB_EXTRACT data extraction version: 3.000
ADSC data collection version: Quantum
HKL-2000 data reduction
HKL-2000 data scaling