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Staphylococcus aureus RNase HII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ETJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 0.15M ammonium sulfate, 0.1M MES, 15%(w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.61 52.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.83 α = 90 b = 61.83 β = 90 c = 163.26 γ = 90
Symmetry Space Group P 43 21 2
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 ADSC QUANTUM 315r 2015-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.987 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 57.82 99.8 18.7 14.3 16871
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 (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 2ETJ 2.2 50 15960 849 99.64 0.23792 0.23566 0.2467 0.28231 0.292 RANDOM 40.426
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] 0.51 0.51 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.354 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_3_deg 15.424 r_long_range_B_refined 8.398 r_long_range_B_other 8.398 r_scangle_other 6.411 r_dihedral_angle_1_deg 6.032 r_mcangle_it 4.927 r_mcangle_other 4.925 r_scbond_it 4.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.354 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_3_deg 15.424 r_long_range_B_refined 8.398 r_long_range_B_other 8.398 r_scangle_other 6.411 r_dihedral_angle_1_deg 6.032 r_mcangle_it 4.927 r_mcangle_other 4.925 r_scbond_it 4.593 r_scbond_other 4.592 r_mcbond_it 3.665 r_mcbond_other 3.651 r_angle_refined_deg 1.365 r_angle_other_deg 1.033 r_chiral_restr 0.086 r_bond_refined_d 0.016 r_bond_other_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 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 1619 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing