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JC polyomavirus VP1 in complex with Fab 98D3
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 7 277.15 0.1 M Ammonium tartrate dibasic pH 7.0, 12% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.85 56.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.97 α = 90 b = 202.31 β = 90 c = 251.66 γ = 90
Symmetry Space Group P 21 21 21
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 2015-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999990 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.75 50 100 0.99 11.99 13.8 225685
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 2.75 2.85 0.68
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 2.75 49.153 225685 11285 99.957 0.21 0.2068 0.21 0.2628 0.2625 45.959
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] -0.966 5.19 -4.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.298 r_dihedral_angle_4_deg 17.467 r_dihedral_angle_3_deg 16.705 r_lrange_it 7.973 r_lrange_other 7.973 r_dihedral_angle_1_deg 7.709 r_mcangle_it 4.584 r_mcangle_other 4.584 r_scangle_it 4.416 r_scangle_other 4.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.298 r_dihedral_angle_4_deg 17.467 r_dihedral_angle_3_deg 16.705 r_lrange_it 7.973 r_lrange_other 7.973 r_dihedral_angle_1_deg 7.709 r_mcangle_it 4.584 r_mcangle_other 4.584 r_scangle_it 4.416 r_scangle_other 4.416 r_mcbond_it 2.863 r_mcbond_other 2.863 r_scbond_it 2.729 r_scbond_other 2.729 r_angle_other_deg 2.441 r_angle_refined_deg 1.676 r_symmetry_nbd_refined 0.257 r_symmetry_xyhbond_nbd_refined 0.239 r_nbd_other 0.232 r_symmetry_nbd_other 0.219 r_nbd_refined 0.196 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_other 0.082 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.066 r_bond_other_d 0.036 r_xyhbond_nbd_other 0.016 r_bond_refined_d 0.006 r_gen_planes_other 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 50676 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing