☰ Navigation Tabs
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 4.5 277.15 1.0 M Sodium Malonate, pH 5.0, 0.1 M Sodium Acetate trihydrate, pH 4.5, 2% (w/v) polyethylene glycol 20,000
Crystal Properties Matthews coefficient Solvent content 2.88 57.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.317 α = 90 b = 113.764 β = 90 c = 155.306 γ = 90
Symmetry Space Group P 21 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 3.2 29.84 99.9 0.116 0.137 0.071 0.999 12.1 6.8 30570
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 3.2 3.37 1.799 2.104 1.082 0.43 7.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7f3e 3.2 29.739 30535 1524 99.81 0.2 0.1977 0.1937 0.2485 0.244 120.427
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] -2.565 2.988 -0.423
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 27.129 r_scangle_it 21.133 r_dihedral_angle_3_deg 18.443 r_dihedral_angle_2_deg 18.126 r_mcangle_it 17.283 r_dihedral_angle_6_deg 15.617 r_scbond_it 13.845 r_mcbond_it 11.399 r_dihedral_angle_1_deg 4.761 r_angle_refined_deg 2.076
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 27.129 r_scangle_it 21.133 r_dihedral_angle_3_deg 18.443 r_dihedral_angle_2_deg 18.126 r_mcangle_it 17.283 r_dihedral_angle_6_deg 15.617 r_scbond_it 13.845 r_mcbond_it 11.399 r_dihedral_angle_1_deg 4.761 r_angle_refined_deg 2.076 r_symmetry_xyhbond_nbd_refined 0.418 r_symmetry_nbd_refined 0.385 r_nbtor_refined 0.314 r_nbd_refined 0.24 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.121 r_gen_planes_refined 0.01 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10010 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing DIALS data processing DIALS data reduction