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BK Polyomavirus VP1 pentamer core (residues 30-299)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MJ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 10% PEG 3350, 0.2 M NaJ, 0.1 M bis-tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.622 α = 90 b = 149.719 β = 90 c = 65.488 γ = 90
Symmetry Space Group P 21 21 2
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 2M 2017-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.976800 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 1.44 50 99.9 0.029 0.999 16.4 13.2 245801 18.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.44 1.49 99.8 0.562 0.62 1.3 11.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4mj0 1.44 50 245801 4820 99.97 0.163 0.1621 0.1681 0.1858 0.1889 22.343
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] -0.144 -0.339 0.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.905 r_dihedral_angle_4_deg 21.872 r_dihedral_angle_3_deg 12.322 r_dihedral_angle_1_deg 7.409 r_lrange_it 6.754 r_lrange_other 6.754 r_scangle_it 2.996 r_scangle_other 2.996 r_mcangle_it 2.215 r_mcangle_other 2.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.905 r_dihedral_angle_4_deg 21.872 r_dihedral_angle_3_deg 12.322 r_dihedral_angle_1_deg 7.409 r_lrange_it 6.754 r_lrange_other 6.754 r_scangle_it 2.996 r_scangle_other 2.996 r_mcangle_it 2.215 r_mcangle_other 2.214 r_scbond_it 1.988 r_scbond_other 1.988 r_angle_refined_deg 1.851 r_angle_other_deg 1.534 r_mcbond_it 1.321 r_mcbond_other 1.321 r_symmetry_nbd_refined 0.371 r_nbd_other 0.276 r_symmetry_xyhbond_nbd_refined 0.255 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.169 r_symmetry_metal_ion_refined 0.168 r_metal_ion_refined 0.16 r_ncsr_local_group_4 0.12 r_ncsr_local_group_10 0.112 r_ncsr_local_group_9 0.106 r_ncsr_local_group_1 0.103 r_ncsr_local_group_2 0.099 r_ncsr_local_group_3 0.099 r_ncsr_local_group_5 0.098 r_ncsr_local_group_6 0.098 r_ncsr_local_group_8 0.098 r_chiral_restr 0.091 r_ncsr_local_group_7 0.085 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.076 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10145 Nucleic Acid Atoms Solvent Atoms 1523 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing