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Structure of apo Human Polyomavirus 12 VP1
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 Tacsimate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.223 α = 90 b = 136.416 β = 109.565 c = 85.379 γ = 90
Symmetry Space Group P 1 21 1
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 2012-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.07 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 1.549 44.05 95.31 0.056 0.999 16.44 3.8 181696 16.35
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 1.549 1.64 0.456 0.855 2.89
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 1.549 44.047 181695 3634 95.103 0.143 0.1427 0.1544 0.1692 0.1799 17.014
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] -0.174 0.067 -0.199 0.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.24 r_dihedral_angle_4_deg 19.238 r_dihedral_angle_3_deg 11.29 r_dihedral_angle_1_deg 6.826 r_lrange_it 4.494 r_lrange_other 4.494 r_scangle_it 2.654 r_scangle_other 2.653 r_mcangle_it 1.869 r_mcangle_other 1.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.24 r_dihedral_angle_4_deg 19.238 r_dihedral_angle_3_deg 11.29 r_dihedral_angle_1_deg 6.826 r_lrange_it 4.494 r_lrange_other 4.494 r_scangle_it 2.654 r_scangle_other 2.653 r_mcangle_it 1.869 r_mcangle_other 1.869 r_scbond_it 1.759 r_scbond_other 1.759 r_angle_refined_deg 1.548 r_angle_other_deg 1.421 r_mcbond_it 1.209 r_mcbond_other 1.203 r_symmetry_nbd_refined 0.358 r_nbd_refined 0.205 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_refined 0.148 r_nbd_other 0.127 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10154 Nucleic Acid Atoms Solvent Atoms 1539 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building