X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VPFPDB ENTRY 1VPF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6HANGING DROP, CRYSTALLIZED FROM 14 % PEG3350, 10% ISOPROPANOL, 0.2 M AMMONIUM ACETATE PH 5.6, vapor diffusion - hanging drop
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.47α = 105.44
b = 68.47β = 93.71
c = 85.82γ = 101.49
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDPRINCETON 2K1996-03-25M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F1CHESSF1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.920940.0449.42.572050
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.9280.80.1271.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1VPF1.9316689017074940.2090.272RESOLUTION SHELLS47.1
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]
-8.560.761.223.091.645.47
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor29.9
p_staggered_tor18.2
p_planar_tor4.1
p_scangle_it3.892
p_mcangle_it2.778
p_scbond_it2.468
p_mcbond_it2.01
p_multtor_nbd0.243
p_xyhbond_nbd0.189
p_singtor_nbd0.179
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor29.9
p_staggered_tor18.2
p_planar_tor4.1
p_scangle_it3.892
p_mcangle_it2.778
p_scbond_it2.468
p_mcbond_it2.01
p_multtor_nbd0.243
p_xyhbond_nbd0.189
p_singtor_nbd0.179
p_chiral_restr0.113
p_planar_d0.032
p_angle_d0.03
p_bond_d0.011
p_angle_deg
p_hb_or_metal_coord
p_plane_restr
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6142
Nucleic Acid Atoms
Solvent Atoms640
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
X-PLORphasing