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High-resolution structure of the nuclease domain from the main replication protein NS1 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 4.5 290 15% PEG 3350
0.1M sodium citrate pH 4.5
0.1M NaCl
0.1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.09 41.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.06 α = 90 b = 49.1 β = 90 c = 74.99 γ = 90
Symmetry Space Group P 2 21 21
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 2013-04-22 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 2.4 45.06 98.44 0.1022 0.1446 0.1022 0.981 7.21 2 6799 28.31
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 2.4 2.486 98.66 0.5331 0.7539 0.5331 0.385 2.43 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6USM 2.4 45.06 1.35 6797 333 98.44 0.2009 0.1981 0.1978 0.2571 0.2543 Random Selection 30.11
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 19.4832 f_angle_d 0.6129 f_chiral_restr 0.0411 f_plane_restr 0.0028 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1337 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection MOSFLM data reduction SCALA data scaling PHASER phasing Coot model building