6Y9I

Structure of apo Chimpanzee Polyomavirus VP1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FMG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293Sodium acetate trihydrate, PEG 3,350, 1,5-Diaminopentane dihydrochloride
Crystal Properties
Matthews coefficientSolvent content
2.4249.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.41α = 68.614
b = 82.19β = 77.361
c = 82.66γ = 77.488
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 2M-F2019-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00003SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.946.4699.40.150.9979.836.9511770932.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9598.90.1350.571.616.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4FMG1.946.456117709588699.5920.1730.17060.213428.057
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]
-0.216-0.6010.3820.19-0.499-0.353
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.319
r_dihedral_angle_4_deg17.55
r_dihedral_angle_3_deg14
r_dihedral_angle_1_deg7.627
r_lrange_it5.792
r_lrange_other5.734
r_scangle_it4.214
r_scangle_other4.214
r_mcangle_it3.283
r_mcangle_other3.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.319
r_dihedral_angle_4_deg17.55
r_dihedral_angle_3_deg14
r_dihedral_angle_1_deg7.627
r_lrange_it5.792
r_lrange_other5.734
r_scangle_it4.214
r_scangle_other4.214
r_mcangle_it3.283
r_mcangle_other3.283
r_scbond_it2.873
r_scbond_other2.873
r_mcbond_it2.278
r_mcbond_other2.274
r_angle_refined_deg1.57
r_angle_other_deg1.314
r_symmetry_nbd_refined0.254
r_nbd_other0.254
r_symmetry_xyhbond_nbd_refined0.22
r_nbd_refined0.192
r_symmetry_nbd_other0.186
r_nbtor_refined0.162
r_xyhbond_nbd_refined0.148
r_symmetry_nbtor_other0.082
r_chiral_restr0.072
r_symmetry_xyhbond_nbd_other0.049
r_metal_ion_refined0.024
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10524
Nucleic Acid Atoms
Solvent Atoms947
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building