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Structure of apo Chimpanzee 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 7 293 Sodium acetate trihydrate, PEG 3,350, 1,5-Diaminopentane dihydrochloride
Crystal Properties Matthews coefficient Solvent content 2.42 49.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.41 α = 68.614 b = 82.19 β = 77.361 c = 82.66 γ = 77.488
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 2019-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00003 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 1.9 46.46 99.4 0.15 0.997 9.83 6.95 117709 32.2
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 1.9 1.95 98.9 0.135 0.57 1.61 6.8
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 (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 1.9 46.456 117709 5886 99.592 0.173 0.1706 0.1778 0.2134 0.2178 28.057
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] -0.216 -0.601 0.382 0.19 -0.499 -0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.319 r_dihedral_angle_4_deg 17.55 r_dihedral_angle_3_deg 14 r_dihedral_angle_1_deg 7.627 r_lrange_it 5.792 r_lrange_other 5.734 r_scangle_it 4.214 r_scangle_other 4.214 r_mcangle_it 3.283 r_mcangle_other 3.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.319 r_dihedral_angle_4_deg 17.55 r_dihedral_angle_3_deg 14 r_dihedral_angle_1_deg 7.627 r_lrange_it 5.792 r_lrange_other 5.734 r_scangle_it 4.214 r_scangle_other 4.214 r_mcangle_it 3.283 r_mcangle_other 3.283 r_scbond_it 2.873 r_scbond_other 2.873 r_mcbond_it 2.278 r_mcbond_other 2.274 r_angle_refined_deg 1.57 r_angle_other_deg 1.314 r_symmetry_nbd_refined 0.254 r_nbd_other 0.254 r_symmetry_xyhbond_nbd_refined 0.22 r_nbd_refined 0.192 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.148 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.049 r_metal_ion_refined 0.024 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10524 Nucleic Acid Atoms Solvent Atoms 947 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building