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JC polyomavirus VP1 in complex with scFv 29B1
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, SITTING DROP 277.15 0.2 M trimethanolamine N-oxide, 0.1 M Tris (pH 8.5), 20% PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.9 57.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.127 α = 90 b = 172.53 β = 104.527 c = 159.71 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 2016-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9794 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 48.5 99.8 0.23 0.99 10.37 7.06 129715
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 3.18 0.95 0.72 2.21
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, 4KQ3 3.102 48.507 117609 5881 99.926 0.225 0.2246 0.2232 0.24 0.2381 44.614
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] 1.331 -0.675 0.489 -1.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.279 r_dihedral_angle_3_deg 15.381 r_dihedral_angle_4_deg 12.846 r_dihedral_angle_1_deg 7.218 r_lrange_it 4.385 r_lrange_other 4.383 r_mcangle_it 4.14 r_mcangle_other 4.14 r_mcbond_it 2.659 r_mcbond_other 2.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.279 r_dihedral_angle_3_deg 15.381 r_dihedral_angle_4_deg 12.846 r_dihedral_angle_1_deg 7.218 r_lrange_it 4.385 r_lrange_other 4.383 r_mcangle_it 4.14 r_mcangle_other 4.14 r_mcbond_it 2.659 r_mcbond_other 2.659 r_scangle_it 2.517 r_scangle_other 2.517 r_angle_other_deg 2.394 r_scbond_it 1.474 r_scbond_other 1.474 r_angle_refined_deg 1.296 r_nbd_other 0.418 r_symmetry_nbd_refined 0.35 r_symmetry_xyhbond_nbd_refined 0.348 r_xyhbond_nbd_other 0.208 r_symmetry_nbd_other 0.206 r_nbd_refined 0.181 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.118 r_symmetry_nbtor_other 0.068 r_chiral_restr 0.049 r_bond_other_d 0.036 r_symmetry_xyhbond_nbd_other 0.018 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37635 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing