6Y65

Structure of apo Goose Hemorrhagic Polyomavirus VP1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293Na nitrate, Na phosphate dibasic, ammonium sulfate, MES, imidazole, PEG 8000, ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.3948.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.29α = 94.048
b = 90.41β = 97.898
c = 100.84γ = 108.064
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 2M-F2017-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00SLSX06DA

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
11.4545.9795.360.0680.99914.263.648752212.8
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)
11.451.5020.7020.7972.16

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-VALUE4FMG1.4545.97487470487595.3790.1490.14840.170313.236
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]
0.648-0.208-0.7070.117-0.675-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.995
r_dihedral_angle_4_deg19.136
r_dihedral_angle_3_deg10.905
r_dihedral_angle_1_deg7.581
r_lrange_it4.578
r_lrange_other4.578
r_scangle_it1.847
r_scangle_other1.847
r_angle_refined_deg1.513
r_angle_other_deg1.421
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.995
r_dihedral_angle_4_deg19.136
r_dihedral_angle_3_deg10.905
r_dihedral_angle_1_deg7.581
r_lrange_it4.578
r_lrange_other4.578
r_scangle_it1.847
r_scangle_other1.847
r_angle_refined_deg1.513
r_angle_other_deg1.421
r_mcangle_it1.402
r_mcangle_other1.402
r_scbond_it1.217
r_scbond_other1.217
r_mcbond_it0.862
r_mcbond_other0.861
r_symmetry_nbd_refined0.306
r_nbd_other0.208
r_nbd_refined0.195
r_symmetry_nbd_other0.184
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.155
r_symmetry_xyhbond_nbd_other0.148
r_symmetry_xyhbond_nbd_refined0.119
r_symmetry_nbtor_other0.083
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20009
Nucleic Acid Atoms
Solvent Atoms3289
Heterogen Atoms434

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building