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JC Polyomavirus genotype 3 VP1 in complex with GD1b oligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NXD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.9 57.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.21 α = 90 b = 96.28 β = 110.28 c = 128.3 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2013-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 30 99.6 2.1 5.7 134124 21.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 95.9 2.1 4.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NXD 1.9 30 127411 6731 99.57 0.15976 0.15835 0.1688 0.1868 0.1939 RANDOM 18.89
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] -0.77 -0.39 0.86 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.592 r_dihedral_angle_4_deg 16.612 r_dihedral_angle_3_deg 11.855 r_dihedral_angle_1_deg 6.439 r_long_range_B_refined 6.024 r_long_range_B_other 6.024 r_scangle_other 3.191 r_scbond_other 2.245 r_scbond_it 2.244 r_mcangle_it 1.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.592 r_dihedral_angle_4_deg 16.612 r_dihedral_angle_3_deg 11.855 r_dihedral_angle_1_deg 6.439 r_long_range_B_refined 6.024 r_long_range_B_other 6.024 r_scangle_other 3.191 r_scbond_other 2.245 r_scbond_it 2.244 r_mcangle_it 1.649 r_mcangle_other 1.649 r_angle_refined_deg 1.336 r_mcbond_it 1.114 r_mcbond_other 1.11 r_angle_other_deg 0.754 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9947 Nucleic Acid Atoms Solvent Atoms 1034 Heterogen Atoms 259
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing XDS data reduction XSCALE data scaling