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Structure of apo Sheep Polyomavirus 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, SITTING DROP 293 KSCN, PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.57 65.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.43 α = 90 b = 130.43 β = 90 c = 221.77 γ = 120
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 2016-08-04 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) 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 2.45 49.77 94.81 0.086 0.998 21.58 8.3 147085
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 2.45 2.538 0.526 0.929 4.69
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4FMG 2.45 49.77 147076 7336 94.803 0.163 0.161 0.1968 0.2309 28.333
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] -18.848 -18.848 37.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.266 r_dihedral_angle_4_deg 21.274 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_1_deg 7.975 r_lrange_it 4.738 r_lrange_other 4.716 r_mcangle_it 3.193 r_mcangle_other 3.193 r_scangle_it 3.026 r_scangle_other 3.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.266 r_dihedral_angle_4_deg 21.274 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_1_deg 7.975 r_lrange_it 4.738 r_lrange_other 4.716 r_mcangle_it 3.193 r_mcangle_other 3.193 r_scangle_it 3.026 r_scangle_other 3.026 r_mcbond_it 2.061 r_mcbond_other 2.061 r_scbond_it 1.978 r_scbond_other 1.978 r_angle_refined_deg 1.534 r_angle_other_deg 1.269 r_nbd_other 0.23 r_symmetry_nbd_other 0.193 r_nbd_refined 0.187 r_symmetry_nbd_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20395 Nucleic Acid Atoms Solvent Atoms 970 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building