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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 3.03 59.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.29 α = 90 b = 68.7 β = 100.4 c = 57.51 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 293 AREA DETECTOR MARRESEARCH mirrors 1996-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 0.9185 EMBL/DESY, HAMBURG X31
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 1.8 15 99.2 0.052 20.5 3.45 35955 35955 23.2
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 1.8 1.83 98.4 0.378 2.96 2.8 1759
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 1.8 15 34158 1796 99.2 0.175 0.17484 0.17246 0.1743 0.21825 RANDOM 26.486
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] -0.89 0.13 2.17 -1.23
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 16.616 r_dihedral_angle_1_deg 7.282 r_scangle_it 6.332 r_sphericity_bonded 5.693 r_scbond_it 4.179 r_mcangle_it 3.229 r_rigid_bond_restr 2.131 r_angle_other_deg 2.112 r_mcbond_it 2.048 r_angle_refined_deg 1.832
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 16.616 r_dihedral_angle_1_deg 7.282 r_scangle_it 6.332 r_sphericity_bonded 5.693 r_scbond_it 4.179 r_mcangle_it 3.229 r_rigid_bond_restr 2.131 r_angle_other_deg 2.112 r_mcbond_it 2.048 r_angle_refined_deg 1.832 r_symmetry_vdw_other 0.307 r_symmetry_vdw_refined 0.303 r_nbd_other 0.254 r_nbd_refined 0.24 r_xyhbond_nbd_refined 0.234 r_symmetry_hbond_refined 0.231 r_chiral_restr 0.123 r_nbtor_other 0.098 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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 2215 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing