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BKPyV VP1 IN COMPLEX WITH VHH016
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished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, SITTING DROP 4.5 293.15 30% (v/v) PEG 400, 100 mM Sodium acetate/Acetic acid pH 4.5,
200 mM Calcium acetate
Crystal Properties Matthews coefficient Solvent content 3.03 59.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.58 α = 90 b = 135.27 β = 97.789 c = 167.83 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 2024-11-02 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 2.59 116.767 99.9 0.0035 0.98 5.1 6.3 160823
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 2.59 2.64 99.9 0.33 0.5 5.9
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 2.593 116.767 160823 8025 99.779 0.213 0.2114 0.2114 0.2357 0.2357 52.939
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] 1.465 0.532 1.111 -2.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.533 r_dihedral_angle_3_deg 13.274 r_lrange_it 8.612 r_lrange_other 8.612 r_dihedral_angle_2_deg 8.246 r_dihedral_angle_1_deg 7.132 r_scangle_it 6.473 r_scangle_other 6.473 r_mcangle_it 5.925 r_mcangle_other 5.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.533 r_dihedral_angle_3_deg 13.274 r_lrange_it 8.612 r_lrange_other 8.612 r_dihedral_angle_2_deg 8.246 r_dihedral_angle_1_deg 7.132 r_scangle_it 6.473 r_scangle_other 6.473 r_mcangle_it 5.925 r_mcangle_other 5.925 r_scbond_it 4.054 r_scbond_other 4.054 r_mcbond_it 3.788 r_mcbond_other 3.788 r_angle_refined_deg 1.306 r_angle_other_deg 0.471 r_nbd_other 0.302 r_symmetry_nbd_refined 0.3 r_symmetry_xyhbond_nbd_refined 0.214 r_metal_ion_refined 0.211 r_nbd_refined 0.207 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.14 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_41 0.083 r_ncsr_local_group_58 0.08 r_ncsr_local_group_9 0.078 r_ncsr_local_group_87 0.078 r_ncsr_local_group_57 0.077 r_ncsr_local_group_84 0.077 r_ncsr_local_group_86 0.077 r_ncsr_local_group_37 0.076 r_ncsr_local_group_44 0.076 r_ncsr_local_group_59 0.075 r_ncsr_local_group_65 0.075 r_ncsr_local_group_90 0.075 r_ncsr_local_group_64 0.073 r_ncsr_local_group_85 0.073 r_ncsr_local_group_17 0.072 r_ncsr_local_group_40 0.072 r_ncsr_local_group_55 0.072 r_ncsr_local_group_60 0.072 r_ncsr_local_group_66 0.072 r_ncsr_local_group_81 0.071 r_ncsr_local_group_89 0.071 r_ncsr_local_group_4 0.07 r_ncsr_local_group_19 0.07 r_ncsr_local_group_38 0.07 r_ncsr_local_group_56 0.07 r_ncsr_local_group_62 0.07 r_ncsr_local_group_23 0.069 r_ncsr_local_group_36 0.069 r_ncsr_local_group_43 0.069 r_ncsr_local_group_48 0.069 r_ncsr_local_group_21 0.068 r_ncsr_local_group_32 0.068 r_ncsr_local_group_63 0.068 r_ncsr_local_group_2 0.067 r_ncsr_local_group_12 0.067 r_ncsr_local_group_31 0.066 r_ncsr_local_group_50 0.066 r_ncsr_local_group_51 0.066 r_ncsr_local_group_77 0.066 r_ncsr_local_group_15 0.065 r_ncsr_local_group_20 0.065 r_ncsr_local_group_24 0.065 r_ncsr_local_group_52 0.065 r_ncsr_local_group_53 0.065 r_ncsr_local_group_61 0.065 r_ncsr_local_group_74 0.065 r_ncsr_local_group_88 0.065 r_ncsr_local_group_47 0.064 r_ncsr_local_group_67 0.064 r_ncsr_local_group_69 0.064 r_ncsr_local_group_79 0.064 r_ncsr_local_group_82 0.064 r_ncsr_local_group_1 0.063 r_chiral_restr 0.062 r_ncsr_local_group_18 0.062 r_ncsr_local_group_34 0.062 r_ncsr_local_group_54 0.062 r_ncsr_local_group_10 0.061 r_ncsr_local_group_16 0.061 r_ncsr_local_group_33 0.061 r_ncsr_local_group_7 0.06 r_ncsr_local_group_35 0.06 r_ncsr_local_group_71 0.06 r_ncsr_local_group_75 0.06 r_ncsr_local_group_46 0.059 r_ncsr_local_group_72 0.059 r_ncsr_local_group_76 0.059 r_ncsr_local_group_80 0.059 r_ncsr_local_group_3 0.058 r_ncsr_local_group_22 0.058 r_ncsr_local_group_27 0.058 r_ncsr_local_group_28 0.058 r_ncsr_local_group_70 0.057 r_ncsr_local_group_6 0.056 r_ncsr_local_group_8 0.056 r_ncsr_local_group_13 0.056 r_ncsr_local_group_39 0.055 r_ncsr_local_group_42 0.055 r_ncsr_local_group_49 0.055 r_ncsr_local_group_68 0.054 r_ncsr_local_group_45 0.053 r_ncsr_local_group_73 0.053 r_ncsr_local_group_11 0.052 r_ncsr_local_group_25 0.052 r_ncsr_local_group_83 0.052 r_ncsr_local_group_5 0.05 r_ncsr_local_group_29 0.049 r_ncsr_local_group_30 0.049 r_ncsr_local_group_14 0.047 r_ncsr_local_group_26 0.046 r_ncsr_local_group_78 0.045 r_xyhbond_nbd_other 0.008 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29190 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement