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JC polyomavirus VP1 from a genotype 3 strain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NXG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.91 57.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.48 α = 90 b = 96.83 β = 110.55 c = 128.22 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 30 99.6 0.125 9.08 4.2 187337 22.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.75 98.4 0.589 2.6 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NXG 1.7 30 177920 9417 99.6 0.15788 0.15683 0.1685 0.17752 0.1873 RANDOM 18.339
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] -0.11 0.16 -0.19 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.832 r_dihedral_angle_4_deg 18.729 r_dihedral_angle_3_deg 11.893 r_long_range_B_refined 6.817 r_long_range_B_other 6.816 r_dihedral_angle_1_deg 6.436 r_scangle_other 3.107 r_scbond_it 2.208 r_scbond_other 2.208 r_mcangle_it 1.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.832 r_dihedral_angle_4_deg 18.729 r_dihedral_angle_3_deg 11.893 r_long_range_B_refined 6.817 r_long_range_B_other 6.816 r_dihedral_angle_1_deg 6.436 r_scangle_other 3.107 r_scbond_it 2.208 r_scbond_other 2.208 r_mcangle_it 1.679 r_mcangle_other 1.679 r_angle_refined_deg 1.408 r_mcbond_it 1.125 r_mcbond_other 1.12 r_angle_other_deg 0.78 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9938 Nucleic Acid Atoms Solvent Atoms 1274 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction PHASER phasing XSCALE data scaling