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Minimal protein-only/RNA-free Ribonuclease P from Hydrogenobacter thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7F3E experimental model PDB 7OG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277.15 2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.92 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.579 α = 90 b = 109.214 β = 90 c = 106.152 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 16M 2020-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03317 APS 23-ID-B
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 2.5 69.72 100 0.304 0.324 0.111 0.991 6.3 8.6 18589
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 2.5 2.6 100 4.001 4.26 1.443 0.434 8.8
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7F3E 2.5 69.72 18563 964 100 0.2 0.2071 0.244 0.25 70.31
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] 5.538 -0.474 -5.063
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 18.365 r_scangle_other 18.311 r_dihedral_angle_3_deg 17.99 r_scbond_it 13.231 r_scbond_other 13.212 r_mcangle_it 11.467 r_mcangle_other 11.467 r_dihedral_angle_2_deg 9.306 r_mcbond_it 9.097 r_mcbond_other 9.089
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 18.365 r_scangle_other 18.311 r_dihedral_angle_3_deg 17.99 r_scbond_it 13.231 r_scbond_other 13.212 r_mcangle_it 11.467 r_mcangle_other 11.467 r_dihedral_angle_2_deg 9.306 r_mcbond_it 9.097 r_mcbond_other 9.089 r_dihedral_angle_1_deg 4.386 r_angle_refined_deg 1.9 r_angle_other_deg 0.57 r_nbd_other 0.226 r_nbd_refined 0.214 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2897 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing DIALS data reduction DIALS data scaling