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Crystal structure of Ribonuclease Sa2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RGG PDB ENTRY 1RGG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 ammonium sulfate, phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.98 α = 90 b = 34.13 β = 109.5 c = 72.27 γ = 90
Symmetry Space Group C 1 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 298 IMAGE PLATE RIGAKU MIRRORS 1997-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 25 98.6 0.063 22.3 3.5 30643 30643 24.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.55 90.2 0.272 2.65 1894
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RGG 1.507 25 29668 975 98.14 0.15 0.15009 0.14933 0.1491 0.1723 RANDOM 22.179
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] -0.55 -0.44 0.9 -0.64
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 10.982 r_dihedral_angle_1_deg 6.464 r_scangle_it 5.178 r_sphericity_bonded 4.639 r_scbond_it 3.507 r_mcangle_it 2.653 r_angle_other_deg 1.745 r_mcbond_it 1.613 r_rigid_bond_restr 1.58 r_angle_refined_deg 1.54
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 10.982 r_dihedral_angle_1_deg 6.464 r_scangle_it 5.178 r_sphericity_bonded 4.639 r_scbond_it 3.507 r_mcangle_it 2.653 r_angle_other_deg 1.745 r_mcbond_it 1.613 r_rigid_bond_restr 1.58 r_angle_refined_deg 1.54 r_nbd_refined 0.299 r_symmetry_vdw_other 0.259 r_nbd_other 0.257 r_xyhbond_nbd_refined 0.203 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.153 r_nbtor_other 0.134 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3024 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing