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BKPyV VP1 IN COMPLEX WITH scFv 319C07
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unpublished
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 293.15 10% (w/v) PEG 6,000 100 mM Bicine pH 9.0
Crystal Properties Matthews coefficient Solvent content 2.96 58.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.25 α = 90 b = 151.89 β = 90 c = 164.69 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 9M 2025-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.987 SOLEIL PROXIMA 2
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 3.7 111.904 99.9 0.023 1 3.7 8.5 29566
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 3.77 3.79 0.4 0.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.726 111.904 29562 1475 99.929 0.249 0.2463 0.2517 0.2941 0.2859 RANDOM 120.484
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] 11.218 -3.154 -8.064
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.883 r_lrange_other 15.883 r_dihedral_angle_6_deg 14.106 r_dihedral_angle_3_deg 13.841 r_mcangle_it 9.512 r_mcangle_other 9.512 r_scangle_it 8.882 r_scangle_other 8.882 r_dihedral_angle_1_deg 6.999 r_dihedral_angle_2_deg 6.203
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 15.883 r_lrange_other 15.883 r_dihedral_angle_6_deg 14.106 r_dihedral_angle_3_deg 13.841 r_mcangle_it 9.512 r_mcangle_other 9.512 r_scangle_it 8.882 r_scangle_other 8.882 r_dihedral_angle_1_deg 6.999 r_dihedral_angle_2_deg 6.203 r_mcbond_it 5.783 r_mcbond_other 5.781 r_scbond_it 5.247 r_scbond_other 5.246 r_angle_refined_deg 1.245 r_symmetry_xyhbond_nbd_refined 0.588 r_angle_other_deg 0.468 r_symmetry_nbd_refined 0.323 r_nbd_other 0.302 r_symmetry_xyhbond_nbd_other 0.197 r_symmetry_nbd_other 0.186 r_nbd_refined 0.185 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.122 r_ncsr_local_group_1 0.08 r_ncsr_local_group_12 0.079 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_6 0.077 r_ncsr_local_group_11 0.076 r_ncsr_local_group_3 0.074 r_ncsr_local_group_5 0.072 r_ncsr_local_group_2 0.065 r_ncsr_local_group_4 0.063 r_ncsr_local_group_13 0.063 r_chiral_restr 0.062 r_ncsr_local_group_8 0.061 r_ncsr_local_group_10 0.057 r_ncsr_local_group_7 0.056 r_ncsr_local_group_9 0.052 r_ext_dist_refined_b 0.035 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15393 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XSCALE data scaling PHASER phasing