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BK Polyomavirus VP1 mutant E73A
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 293.15 PEG 3.350
Lithium Chloride
HEPES
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.488 α = 90 b = 152.305 β = 90 c = 62.578 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 2020-09-03 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 1.887 50 99.9 0.99 15.63 13.4 111193
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 1.887 1.935 0.69
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 1.887 47.898 111193 5587 99.888 0.176 0.1745 0.182 0.2115 0.2134 30.446
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] 0.73 -0.532 -0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.614 r_dihedral_angle_4_deg 23.263 r_dihedral_angle_3_deg 13.2 r_dihedral_angle_1_deg 7.686 r_lrange_it 5.686 r_lrange_other 5.668 r_scangle_it 4.423 r_scangle_other 4.422 r_mcangle_it 3.539 r_mcangle_other 3.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.614 r_dihedral_angle_4_deg 23.263 r_dihedral_angle_3_deg 13.2 r_dihedral_angle_1_deg 7.686 r_lrange_it 5.686 r_lrange_other 5.668 r_scangle_it 4.423 r_scangle_other 4.422 r_mcangle_it 3.539 r_mcangle_other 3.538 r_scbond_it 3.092 r_scbond_other 3.092 r_mcbond_it 2.6 r_mcbond_other 2.599 r_angle_refined_deg 1.62 r_angle_other_deg 1.329 r_nbd_other 0.252 r_symmetry_nbd_refined 0.203 r_nbd_refined 0.2 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.106 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.024 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 9792 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction REFMAC phasing Coot model building XSCALE data scaling