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JC Mad-1 polyomavirus VP1 in complex with GM2 oligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NXG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.91 57.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.49 α = 90 b = 95.68 β = 110.3 c = 129.72 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 6M 2012-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.11 30 99.3 9.1 4.2 99141 30.4
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 2.11 2.16 99.3 2.3 3.8
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 3NXG 2.11 30 94182 4959 99.28 0.17387 0.17224 0.1793 0.20499 0.2107 RANDOM 25.575
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] -0.21 -0.37 0.44 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.852 r_dihedral_angle_4_deg 13.553 r_dihedral_angle_3_deg 12.395 r_dihedral_angle_1_deg 6.492 r_long_range_B_refined 5.258 r_long_range_B_other 5.258 r_scangle_other 1.445 r_angle_refined_deg 1.324 r_mcangle_it 0.987 r_mcangle_other 0.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.852 r_dihedral_angle_4_deg 13.553 r_dihedral_angle_3_deg 12.395 r_dihedral_angle_1_deg 6.492 r_long_range_B_refined 5.258 r_long_range_B_other 5.258 r_scangle_other 1.445 r_angle_refined_deg 1.324 r_mcangle_it 0.987 r_mcangle_other 0.987 r_scbond_it 0.885 r_scbond_other 0.884 r_angle_other_deg 0.746 r_mcbond_it 0.59 r_mcbond_other 0.59 r_chiral_restr 0.078 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 9920 Nucleic Acid Atoms Solvent Atoms 891 Heterogen Atoms 271
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction