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BK Polyomavirus VP1 mutant VQQ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 PEG 3.350
Lithium Chloride
HEPES
Crystal Properties Matthews coefficient Solvent content 2.32 47.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.691 α = 90 b = 152.596 β = 90 c = 62.746 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-F 2021-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.798 50 99.9 0.999 13.4 13.4 129677
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 1.798 1.862 0.576
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 4MJ1 1.798 48.463 129673 6484 99.921 0.173 0.1716 0.1802 0.2097 0.2145 26.89
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] 0.359 -0.024 -0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.991 r_dihedral_angle_4_deg 21.176 r_dihedral_angle_3_deg 13.2 r_dihedral_angle_1_deg 7.482 r_lrange_it 5.736 r_lrange_other 5.715 r_scangle_it 4.517 r_scangle_other 4.516 r_mcangle_it 3.318 r_mcangle_other 3.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.991 r_dihedral_angle_4_deg 21.176 r_dihedral_angle_3_deg 13.2 r_dihedral_angle_1_deg 7.482 r_lrange_it 5.736 r_lrange_other 5.715 r_scangle_it 4.517 r_scangle_other 4.516 r_mcangle_it 3.318 r_mcangle_other 3.317 r_scbond_it 3.073 r_scbond_other 3.073 r_mcbond_it 2.399 r_mcbond_other 2.397 r_angle_refined_deg 1.647 r_angle_other_deg 1.356 r_nbd_other 0.223 r_nbd_refined 0.2 r_symmetry_nbd_other 0.182 r_symmetry_nbd_refined 0.181 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.155 r_xyhbond_nbd_refined 0.147 r_symmetry_xyhbond_nbd_other 0.083 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9839 Nucleic Acid Atoms Solvent Atoms 666 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction REFMAC phasing Coot model building XSCALE data scaling