☰ Navigation Tabs
Crystal structure of Porcine Circovirus type II Rep ATPase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1M BIS-TRIS PH6.0, 0.2M Li2SO4, 22% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.25 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.92 α = 90 b = 103.93 β = 109.9 c = 76.85 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 100 CCD Nonius Kappa CCD 2022-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.95915 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 59.33 100 0.999 16.3 6.7 50956
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 0.944
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 59.33 48441 2491 99.97 0.29073 0.28924 0.2827 0.31926 0.3032 RANDOM 44.462
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 0.12 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.111 r_long_range_B_refined 13.806 r_long_range_B_other 13.806 r_dihedral_angle_2_deg 11.827 r_scangle_other 8.87 r_dihedral_angle_1_deg 8.212 r_mcangle_it 7.595 r_mcangle_other 7.595 r_scbond_it 5.734 r_scbond_other 5.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.111 r_long_range_B_refined 13.806 r_long_range_B_other 13.806 r_dihedral_angle_2_deg 11.827 r_scangle_other 8.87 r_dihedral_angle_1_deg 8.212 r_mcangle_it 7.595 r_mcangle_other 7.595 r_scbond_it 5.734 r_scbond_other 5.733 r_mcbond_it 4.966 r_mcbond_other 4.966 r_angle_refined_deg 1.566 r_angle_other_deg 0.5 r_chiral_restr 0.071 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6898 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing