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BK Polyomavirus VP1 pentamer core(residues 26-299) mutant C104S
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 298 17 % PEG 3350, 0.3 M sodium formate
Crystal Properties Matthews coefficient Solvent content 2.2 44.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.067 α = 90 b = 135.717 β = 94.981 c = 156.434 γ = 90
Symmetry Space Group P 1 21 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-F 2020-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9126 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.47 102.35 96.6 0.06 0.072 0.039 0.997 9.2 2.8 418028
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 1.47 1.55 82.6 0.387 0.7 1.1 1.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4mj0 1.474 102.35 417886 20576 96.557 0.182 0.1807 0.1971 0.2165 21.011
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] 0.158 -0.157 -0.195 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 22.847 r_dihedral_angle_3_deg 12.158 r_dihedral_angle_1_deg 7.339 r_lrange_it 5.218 r_lrange_other 5.218 r_scangle_it 3.855 r_scangle_other 3.855 r_mcangle_it 2.764 r_mcangle_other 2.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 22.847 r_dihedral_angle_3_deg 12.158 r_dihedral_angle_1_deg 7.339 r_lrange_it 5.218 r_lrange_other 5.218 r_scangle_it 3.855 r_scangle_other 3.855 r_mcangle_it 2.764 r_mcangle_other 2.764 r_scbond_it 2.6 r_scbond_other 2.6 r_mcbond_it 1.857 r_mcbond_other 1.857 r_angle_refined_deg 1.637 r_angle_other_deg 1.457 r_symmetry_nbd_refined 0.246 r_symmetry_xyhbond_nbd_other 0.234 r_nbd_other 0.22 r_nbd_refined 0.214 r_symmetry_nbd_other 0.181 r_symmetry_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.167 r_ncsr_local_group_41 0.097 r_ncsr_local_group_45 0.096 r_ncsr_local_group_16 0.09 r_ncsr_local_group_42 0.088 r_ncsr_local_group_24 0.086 r_ncsr_local_group_17 0.085 r_ncsr_local_group_27 0.085 r_ncsr_local_group_23 0.084 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_11 0.081 r_ncsr_local_group_21 0.08 r_chiral_restr 0.078 r_ncsr_local_group_10 0.078 r_ncsr_local_group_29 0.078 r_ncsr_local_group_30 0.078 r_ncsr_local_group_13 0.077 r_ncsr_local_group_38 0.077 r_ncsr_local_group_1 0.076 r_ncsr_local_group_8 0.076 r_ncsr_local_group_18 0.076 r_ncsr_local_group_20 0.075 r_ncsr_local_group_39 0.074 r_ncsr_local_group_12 0.072 r_ncsr_local_group_34 0.072 r_ncsr_local_group_15 0.071 r_ncsr_local_group_36 0.071 r_ncsr_local_group_44 0.071 r_ncsr_local_group_3 0.069 r_ncsr_local_group_26 0.069 r_ncsr_local_group_2 0.068 r_ncsr_local_group_14 0.068 r_ncsr_local_group_43 0.068 r_ncsr_local_group_19 0.067 r_ncsr_local_group_9 0.066 r_ncsr_local_group_6 0.065 r_ncsr_local_group_7 0.063 r_ncsr_local_group_28 0.063 r_ncsr_local_group_40 0.063 r_ncsr_local_group_25 0.062 r_ncsr_local_group_31 0.061 r_ncsr_local_group_33 0.061 r_ncsr_local_group_37 0.061 r_ncsr_local_group_4 0.059 r_ncsr_local_group_5 0.059 r_ncsr_local_group_32 0.057 r_ncsr_local_group_22 0.055 r_ncsr_local_group_35 0.05 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20368 Nucleic Acid Atoms Solvent Atoms 1978 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing