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Crystal structure of murine polyomavirus PTA strain VP1
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 7.5 277.15 0.1 M HEPES, pH 7.5
1 M sodium phosphate monobasic
0.8 M potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 4.4 72.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.61 α = 90 b = 219.61 β = 90 c = 99.82 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 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 1.64 50 99.9 0.105 10.5 5 334981
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 1.64 1.68 99.9 0.687 2.3 4.8
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 1VPN 1.64 48.15 324802 10169 99.86 0.1589 0.1585 0.1561 0.173 0.1707 RANDOM 20.739
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 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.372 r_dihedral_angle_4_deg 19.198 r_dihedral_angle_3_deg 10.776 r_dihedral_angle_1_deg 5.835 r_angle_refined_deg 1.155 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10863 Nucleic Acid Atoms Solvent Atoms 1812 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHENIX phasing