X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VPEPDB ENTRY 1VPE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.3291sodium formate, acetate, pH 5.3, microbatch, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.754.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.175α = 90
b = 143.175β = 90
c = 75.641γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS Vmirrors2003-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.00SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.53099.90.0510.04421.47.4614081514081517.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5599.30.1920.1697.895.3813920

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1VPE1.530140815140777703199.70.2020.2020.2010.215RANDOM19.1
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.310.490.31-0.62
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.6
c_scangle_it2.71
c_scbond_it1.84
c_mcangle_it1.58
c_angle_deg1.3
c_mcbond_it1.03
c_improper_angle_d0.85
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5898
Nucleic Acid Atoms
Solvent Atoms734
Heterogen Atoms27

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing