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Structure of the N-terminal nuclease and origin binding domain of Human Parvovirus B19
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6USM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 273 2.5 M sodium chloride
0.1 M Tris-HCl pH 7.0
200 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 3.87 68.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.71 α = 90 b = 106.71 β = 90 c = 59.59 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS PILATUS3 6M 2020-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 3.5 50.08 98.68 0.07557 0.1072 0.07557 0.993 5.37 2 5099 91.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.625 97.41 0.4226 0.5977 0.4226 0.89 1.67 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6USM 3.5 50.08 1.34 5076 508 98.77 0.2658 0.2622 0.2991 0.2733 94.33
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.0876 f_angle_d 0.8672 f_chiral_restr 0.0557 f_plane_restr 0.0057 f_bond_d 0.0036
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1289 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection MOSFLM data reduction SCALA data scaling PHASER phasing Coot model building