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BK Polyomavirus VP1 pentamer fusion with long C-terminal extended arm
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, SITTING DROP 6.5 298 33 % EDO_P8K,100 mM Morpheus buffer 1 (pH 6.5), 50 mM Morpheus NPS
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 234.297 α = 90 b = 97.205 β = 98.379 c = 146.166 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 2018-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976251 ESRF ID30B
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 2.48 90 99.04 0.1105 0.984 6.29 3.7 113999 39.25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.57 98.22 0.6
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 2.484 90 113577 5586 99.066 0.206 0.205 0.2333 0.2367 40.569
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] -1.597 1.147 1.432 -0.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.007 r_dihedral_angle_4_deg 19.226 r_dihedral_angle_3_deg 15.086 r_dihedral_angle_1_deg 7.842 r_lrange_it 5.691 r_lrange_other 5.676 r_scangle_it 3.807 r_scangle_other 3.807 r_mcangle_it 3.313 r_mcangle_other 3.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.007 r_dihedral_angle_4_deg 19.226 r_dihedral_angle_3_deg 15.086 r_dihedral_angle_1_deg 7.842 r_lrange_it 5.691 r_lrange_other 5.676 r_scangle_it 3.807 r_scangle_other 3.807 r_mcangle_it 3.313 r_mcangle_other 3.313 r_scbond_it 2.341 r_scbond_other 2.341 r_mcbond_it 2.048 r_mcbond_other 2.048 r_angle_refined_deg 1.574 r_angle_other_deg 1.246 r_symmetry_xyhbond_nbd_refined 0.253 r_nbd_other 0.251 r_symmetry_nbd_refined 0.239 r_nbd_refined 0.2 r_symmetry_nbd_other 0.185 r_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.159 r_metal_ion_refined 0.134 r_ncsr_local_group_27 0.093 r_ncsr_local_group_21 0.088 r_ncsr_local_group_32 0.086 r_ncsr_local_group_26 0.085 r_ncsr_local_group_6 0.084 r_ncsr_local_group_20 0.083 r_ncsr_local_group_23 0.083 r_ncsr_local_group_19 0.079 r_ncsr_local_group_31 0.079 r_ncsr_local_group_5 0.078 r_ncsr_local_group_24 0.078 r_ncsr_local_group_29 0.078 r_ncsr_local_group_33 0.077 r_ncsr_local_group_41 0.077 r_ncsr_local_group_30 0.076 r_symmetry_nbtor_other 0.075 r_ncsr_local_group_11 0.075 r_ncsr_local_group_38 0.075 r_ncsr_local_group_14 0.074 r_ncsr_local_group_28 0.074 r_ncsr_local_group_3 0.073 r_ncsr_local_group_10 0.073 r_ncsr_local_group_22 0.073 r_xyhbond_nbd_other 0.072 r_ncsr_local_group_42 0.072 r_ncsr_local_group_12 0.071 r_ncsr_local_group_18 0.071 r_ncsr_local_group_40 0.071 r_ncsr_local_group_8 0.07 r_ncsr_local_group_13 0.07 r_ncsr_local_group_35 0.07 r_ncsr_local_group_43 0.07 r_ncsr_local_group_2 0.069 r_ncsr_local_group_15 0.069 r_ncsr_local_group_34 0.068 r_ncsr_local_group_37 0.068 r_ncsr_local_group_44 0.068 r_ncsr_local_group_9 0.067 r_ncsr_local_group_25 0.067 r_chiral_restr 0.066 r_ncsr_local_group_1 0.065 r_ncsr_local_group_7 0.065 r_ncsr_local_group_39 0.065 r_ncsr_local_group_16 0.063 r_ncsr_local_group_4 0.062 r_ncsr_local_group_45 0.062 r_symmetry_xyhbond_nbd_other 0.061 r_ncsr_local_group_36 0.06 r_ncsr_local_group_17 0.055 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21385 Nucleic Acid Atoms Solvent Atoms 863 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing