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Crystal structure of murine polyomavirus RA strain VP1 in complex with the GT1a glycan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 1.7 M ammonium sulfate
4.9% (v/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 4.39 71.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.55 α = 90 b = 219.55 β = 90 c = 99.6 γ = 120
Symmetry Space Group P 31 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-F 2012-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99987 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.71 50 99.7 0.074 15.71 4.3 294839
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.75 99.9 0.741 2.17 3.9
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 1VPN 1.71 48.22 285887 8954 99.82 0.1554 0.1549 0.1537 0.1724 0.1706 RANDOM 23.246
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] 0.08 0.08 0.08 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.309 r_dihedral_angle_4_deg 18.698 r_dihedral_angle_3_deg 11.355 r_dihedral_angle_1_deg 5.705 r_angle_refined_deg 1.107 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10897 Nucleic Acid Atoms Solvent Atoms 1885 Heterogen Atoms 559
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHENIX phasing