X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help


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
Space Group P 21 21 21


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

Data Collection

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


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 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