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Structure of Human Polyomavirus 12 VP1 in complex with 3'-Sialyllactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Ammonium acetate, Bis-Tris, 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.57 52.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.322 α = 90 b = 141.724 β = 90 c = 251.302 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-F 2013-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 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 1.798 47.37 99.4 0.125 0.999 12.21 7.04 274251 33.3
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 1.798 1.91 1.77 0.725 1.34
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 4FMG 1.798 47.37 274154 2741 99.412 0.204 0.2035 0.2104 0.243 0.2506 30.486
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] 1.259 1.898 -3.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.246 r_dihedral_angle_4_deg 21.357 r_dihedral_angle_3_deg 12.819 r_dihedral_angle_1_deg 7.175 r_lrange_it 5.25 r_lrange_other 5.17 r_scangle_it 3.959 r_scangle_other 3.959 r_mcangle_it 3.217 r_mcangle_other 3.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.246 r_dihedral_angle_4_deg 21.357 r_dihedral_angle_3_deg 12.819 r_dihedral_angle_1_deg 7.175 r_lrange_it 5.25 r_lrange_other 5.17 r_scangle_it 3.959 r_scangle_other 3.959 r_mcangle_it 3.217 r_mcangle_other 3.217 r_scbond_it 2.787 r_scbond_other 2.787 r_mcbond_it 2.422 r_mcbond_other 2.422 r_angle_refined_deg 1.629 r_angle_other_deg 1.31 r_symmetry_xyhbond_nbd_refined 0.47 r_symmetry_nbd_refined 0.245 r_nbd_other 0.213 r_nbd_refined 0.199 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19801 Nucleic Acid Atoms Solvent Atoms 1825 Heterogen Atoms 312
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building