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BKPyV VP1 IN COMPLEX WITH VHH017
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished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 7.5 293.15 10% w/v PEG4000, 20% v/v glycerol, 0.1M
MOPS/HEPES-Na pH 7.5, 0.02 M sodium L-glutamate, 0.02M DL-alanine, 0.02M glycine,
0.02M DL-lysine HCl, 0.02M DL-serine
Crystal Properties Matthews coefficient Solvent content 2.69 54.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.83 α = 90 b = 152.361 β = 94.398 c = 91.933 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 EIGER X 9M 2022-12-18 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 2.49 47.3 99.3 0.104 0.99 6.5 3.6 81528
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 2.49 2.52 80.1 0.29 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.492 47.276 81528 2039 99.246 0.194 0.1928 0.192 0.2248 0.2235 46.102
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] -3.316 0.447 0.801 2.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.447 r_dihedral_angle_3_deg 12.669 r_lrange_it 6.532 r_lrange_other 6.53 r_dihedral_angle_1_deg 6.225 r_dihedral_angle_2_deg 5.268 r_scangle_it 4.465 r_scangle_other 4.464 r_mcangle_other 3.574 r_mcangle_it 3.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.447 r_dihedral_angle_3_deg 12.669 r_lrange_it 6.532 r_lrange_other 6.53 r_dihedral_angle_1_deg 6.225 r_dihedral_angle_2_deg 5.268 r_scangle_it 4.465 r_scangle_other 4.464 r_mcangle_other 3.574 r_mcangle_it 3.573 r_scbond_it 2.645 r_scbond_other 2.645 r_mcbond_it 2.141 r_mcbond_other 2.141 r_angle_refined_deg 0.988 r_angle_other_deg 0.358 r_symmetry_xyhbond_nbd_refined 0.348 r_nbd_other 0.228 r_symmetry_nbd_other 0.19 r_nbd_refined 0.184 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.139 r_symmetry_nbd_refined 0.136 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_12 0.076 r_ncsr_local_group_18 0.073 r_ncsr_local_group_15 0.072 r_ncsr_local_group_19 0.072 r_ncsr_local_group_13 0.07 r_ncsr_local_group_1 0.068 r_ncsr_local_group_4 0.068 r_ncsr_local_group_8 0.068 r_ncsr_local_group_11 0.067 r_ncsr_local_group_7 0.066 r_ncsr_local_group_2 0.065 r_ncsr_local_group_3 0.063 r_ncsr_local_group_5 0.061 r_ncsr_local_group_9 0.059 r_ncsr_local_group_6 0.058 r_ncsr_local_group_10 0.057 r_ncsr_local_group_17 0.057 r_ncsr_local_group_20 0.055 r_ncsr_local_group_14 0.049 r_chiral_restr 0.048 r_ncsr_local_group_16 0.038 r_symmetry_xyhbond_nbd_other 0.024 r_xyhbond_nbd_other 0.009 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14978 Nucleic Acid Atoms Solvent Atoms 690 Heterogen Atoms 157
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing