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BK polyomavirus VP1 in complex with scFv 29B1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MJ1 4MJ1, 4KQ3 experimental model PDB 4KQ3 4MJ1, 4KQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 0.1 M sodium malonate (pH 5.5), 14.4% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.05 59.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.588 α = 92.315 b = 114.614 β = 105.996 c = 142.373 γ = 111.407
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 2M-F 2017-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.6 49.2 94.8 0.17 0.98 5.9 1.8 181005 34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.81 0.74 0.61 1.4
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, 4KQ3 2.6 48.444 180984 1810 91.922 0.247 0.2471 0.2487 0.2724 0.2754 26.747
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] -1.103 -0.183 0.491 -1.288 0.287 1.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.569 r_dihedral_angle_4_deg 21.388 r_dihedral_angle_3_deg 16.608 r_lrange_other 7.781 r_lrange_it 7.778 r_dihedral_angle_1_deg 6.792 r_scangle_it 4.507 r_scangle_other 4.507 r_mcangle_it 4.158 r_mcangle_other 4.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.569 r_dihedral_angle_4_deg 21.388 r_dihedral_angle_3_deg 16.608 r_lrange_other 7.781 r_lrange_it 7.778 r_dihedral_angle_1_deg 6.792 r_scangle_it 4.507 r_scangle_other 4.507 r_mcangle_it 4.158 r_mcangle_other 4.158 r_scbond_it 2.848 r_scbond_other 2.848 r_mcbond_it 2.639 r_mcbond_other 2.639 r_angle_other_deg 2.376 r_angle_refined_deg 1.438 r_nbd_other 0.285 r_symmetry_xyhbond_nbd_refined 0.278 r_symmetry_nbd_other 0.223 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.209 r_symmetry_nbd_refined 0.199 r_symmetry_xyhbond_nbd_other 0.189 r_nbtor_refined 0.166 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.064 r_xyhbond_nbd_other 0.044 r_bond_other_d 0.037 r_bond_refined_d 0.007 r_gen_planes_other 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36978 Nucleic Acid Atoms Solvent Atoms 726 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing