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BK Polyomavirus VP1 mutant E73Q
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 2.34 47.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.253 α = 90 b = 153.039 β = 90 c = 62.801 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 2019-04-07 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 1.853 50 99.6 0.999 13.99 13.2 119532
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 1.853 1.919 0.737
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 4MJ1 1.853 48.545 119147 5959 99.602 0.192 0.1902 0.229 0.1989 28.682
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] -1.062 1.152 -0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_4_deg 22.902 r_dihedral_angle_3_deg 12.943 r_dihedral_angle_1_deg 7.679 r_lrange_it 5.173 r_lrange_other 5.123 r_scangle_it 3.958 r_scangle_other 3.958 r_mcangle_it 3.233 r_mcangle_other 3.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_4_deg 22.902 r_dihedral_angle_3_deg 12.943 r_dihedral_angle_1_deg 7.679 r_lrange_it 5.173 r_lrange_other 5.123 r_scangle_it 3.958 r_scangle_other 3.958 r_mcangle_it 3.233 r_mcangle_other 3.232 r_scbond_it 2.744 r_scbond_other 2.744 r_mcbond_it 2.339 r_mcbond_other 2.339 r_angle_refined_deg 1.601 r_angle_other_deg 1.307 r_symmetry_nbd_refined 0.22 r_nbd_other 0.207 r_nbd_refined 0.202 r_symmetry_nbd_other 0.177 r_symmetry_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.057 r_bond_refined_d 0.009 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 9766 Nucleic Acid Atoms Solvent Atoms 841 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction REFMAC phasing Coot model building XSCALE data scaling