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JC polyomavirus VP1 in complex with scFv 27C11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NXG 3NXG, 4KQ3 experimental model PDB 4KQ3 3NXG, 4KQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 100 mM potassium phosphate monohydrate / potassium phosphate dihydrate pH 6.0, 10% (w/v) PEG 8000, 686 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.74 55.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.09 α = 100.913 b = 96.11 β = 93.012 c = 190.41 γ = 113.835
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 2016-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99 SLS X06SA
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 1.9 48.5 89.9 0.1 0.99 9.27 3.83 465782
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 1.9 2.01 1.19 0.5 1.15
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3NXG, 4KQ3 1.9 47.809 465782 23290 97.59 0.185 0.1835 0.2164 0.2215 36.13
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] 1.146 1.239 -0.33 -0.626 -0.557 -0.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.253 r_dihedral_angle_4_deg 15.824 r_dihedral_angle_3_deg 13.666 r_lrange_it 8.463 r_lrange_other 8.452 r_dihedral_angle_1_deg 6.74 r_scangle_it 6.373 r_scangle_other 6.373 r_mcangle_it 4.516 r_mcangle_other 4.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.253 r_dihedral_angle_4_deg 15.824 r_dihedral_angle_3_deg 13.666 r_lrange_it 8.463 r_lrange_other 8.452 r_dihedral_angle_1_deg 6.74 r_scangle_it 6.373 r_scangle_other 6.373 r_mcangle_it 4.516 r_mcangle_other 4.516 r_scbond_it 4.381 r_scbond_other 4.381 r_mcbond_other 3.249 r_mcbond_it 3.248 r_angle_other_deg 2.36 r_angle_refined_deg 1.604 r_symmetry_nbd_other 0.231 r_nbd_other 0.229 r_nbd_refined 0.195 r_symmetry_nbd_refined 0.185 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.16 r_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_other 0.138 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.073 r_bond_other_d 0.037 r_bond_refined_d 0.01 r_gen_planes_other 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37890 Nucleic Acid Atoms Solvent Atoms 2249 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing