☰ Navigation Tabs
Crystal structure of murine polyomavirus PTA strain VP1 in complex with the DSLNT 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 8.5 277.15 0.1 M HEPES pH 8.5, 1 M sodium phosphate monobasic, 0.8 M potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 4.41 72.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.73 α = 90 b = 219.73 β = 90 c = 100 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 CCD ADSC QUANTUM 210 2012-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 1.0 ESRF ID14-1
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 1.87 50 99.8 0.152 7.6 3.7 226957
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 1.87 1.92 99.8 0.691 3.7
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 1.87 48.36 220105 6850 99.78 0.1544 0.1538 0.1533 0.1756 0.1743 RANDOM 21.617
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] -0.03 -0.03 -0.03 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.511 r_dihedral_angle_4_deg 20.153 r_dihedral_angle_3_deg 11.258 r_dihedral_angle_1_deg 5.723 r_angle_refined_deg 1.196 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10806 Nucleic Acid Atoms Solvent Atoms 1616 Heterogen Atoms 218
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction