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BK Polyomavirus VP1 mutant N-Q
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 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.462 α = 90 b = 155.959 β = 92.636 c = 141.322 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 2M-F 2021-04-15 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 2.006 50 94.81 0.994 8.35 6.6 164438
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 2.006 2.082 0.852
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 2.006 48.784 164438 8246 94.538 0.183 0.18 0.1882 0.232 0.2344 28.332
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] -0.554 -0.485 0.338 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.535 r_dihedral_angle_4_deg 22.145 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_1_deg 7.982 r_lrange_it 5.35 r_lrange_other 5.34 r_scangle_it 4.195 r_scangle_other 4.195 r_mcangle_it 3.314 r_mcangle_other 3.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.535 r_dihedral_angle_4_deg 22.145 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_1_deg 7.982 r_lrange_it 5.35 r_lrange_other 5.34 r_scangle_it 4.195 r_scangle_other 4.195 r_mcangle_it 3.314 r_mcangle_other 3.314 r_scbond_it 2.915 r_scbond_other 2.915 r_mcbond_it 2.363 r_mcbond_other 2.362 r_angle_refined_deg 1.714 r_angle_other_deg 1.258 r_symmetry_xyhbond_nbd_refined 0.273 r_nbd_refined 0.2 r_symmetry_nbd_other 0.176 r_nbd_other 0.167 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.144 r_symmetry_nbd_refined 0.128 r_symmetry_xyhbond_nbd_other 0.081 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.072 r_bond_refined_d 0.01 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 19642 Nucleic Acid Atoms Solvent Atoms 1023 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing Coot model building