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Crystal structure of murine polyomavirus RA strain VP1 in complex with the GD1a glycan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 1.5 M ammonium sulfate, 6% (v/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 4.36 71.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.06 α = 90 b = 219.06 β = 90 c = 99.4 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 1.0 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 1.9 50 99 0.111 11.3 2.9 212126
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 1.9 1.95 99.1 0.717 1.9 2.8
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 5CPU 1.9 48.12 205733 6393 98.91 0.1553 0.1546 0.1545 0.1784 0.1781 RANDOM 21.961
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] 0.15 0.15 0.15 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.647 r_dihedral_angle_4_deg 19.284 r_dihedral_angle_3_deg 11.528 r_dihedral_angle_1_deg 5.925 r_angle_refined_deg 1.192 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10873 Nucleic Acid Atoms Solvent Atoms 1793 Heterogen Atoms 463
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHENIX phasing