3BWR

SV40 VP1 pentamer in complex with GM1 oligosaccharide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293RESERVOIR: 0.1 M TRIS, PH 8.5, 24% PEG3350. DROP: RESERVOIR MIXED 4:1 WITH 30% ETHYLENE GLYCOL. THIS WAS MIXED 1:1 WITH VP1 (11 MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7455.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.764α = 90
b = 93.087β = 105.6
c = 118.882γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
12.253089.80.09711.28.76838733.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3353.80.2761.94.84050

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1SVA2.2529.7668387686889.80.192060.187430.23318RANDOM33.589
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]
-2.26-2.62.29-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.474
r_dihedral_angle_3_deg13.741
r_dihedral_angle_4_deg13.641
r_dihedral_angle_1_deg5.514
r_scangle_it4.006
r_mcangle_it3.314
r_scbond_it2.728
r_mcbond_it2.082
r_angle_refined_deg0.814
r_symmetry_vdw_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.474
r_dihedral_angle_3_deg13.741
r_dihedral_angle_4_deg13.641
r_dihedral_angle_1_deg5.514
r_scangle_it4.006
r_mcangle_it3.314
r_scbond_it2.728
r_mcbond_it2.082
r_angle_refined_deg0.814
r_symmetry_vdw_refined0.32
r_nbtor_refined0.309
r_nbd_refined0.192
r_symmetry_hbond_refined0.11
r_xyhbond_nbd_refined0.104
r_bond_refined_d0.005
r_chiral_restr0.003
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10160
Nucleic Acid Atoms
Solvent Atoms855
Heterogen Atoms228

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing