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JC polyomavirus VP1 in complex with Fab 27C2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NXG 3NXG, 5BVJ experimental model PDB 5BVJ 3NXG, 5BVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.1 M Ammonium citrate tribasic pH 7.0, 12% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.38 63.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.07 α = 90 b = 110.44 β = 93.115 c = 158.21 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 93 PIXEL DECTRIS PILATUS 2M-F 2016-02-14 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 3.15 49.007 99.6 0.32 0.98 9.49 7.03 81593
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 3.15 3.34 1.05 0.53 1.6
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 3NXG, 5BVJ 3.15 49.007 81570 4079 99.682 0.213 0.212 0.2132 0.2407 0.2398 45.462
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] 6.326 0.325 -2.023 -4.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.411 r_dihedral_angle_4_deg 17.891 r_dihedral_angle_3_deg 15.348 r_lrange_it 11.549 r_lrange_other 11.549 r_dihedral_angle_1_deg 7.859 r_mcangle_it 7.403 r_mcangle_other 7.403 r_scangle_it 7.285 r_scangle_other 7.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.411 r_dihedral_angle_4_deg 17.891 r_dihedral_angle_3_deg 15.348 r_lrange_it 11.549 r_lrange_other 11.549 r_dihedral_angle_1_deg 7.859 r_mcangle_it 7.403 r_mcangle_other 7.403 r_scangle_it 7.285 r_scangle_other 7.285 r_mcbond_it 4.689 r_mcbond_other 4.689 r_scbond_it 4.628 r_scbond_other 4.628 r_angle_other_deg 2.444 r_angle_refined_deg 1.604 r_nbd_other 0.293 r_symmetry_nbd_refined 0.273 r_symmetry_nbd_other 0.224 r_nbd_refined 0.207 r_symmetry_xyhbond_nbd_refined 0.204 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.05 r_bond_other_d 0.037 r_bond_refined_d 0.009 r_gen_planes_other 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21270 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing