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Ultra High Resolution X-ray Structure of Orthorhombic Bovine Pancreatic Ribonuclease at 100K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 277 100mg of powdered Ribonuclease A in 1ml of distilled water dissolved in 2ml of ice cold absolute ethanol.
Crystal Properties Matthews coefficient Solvent content 1.87 34.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.998 α = 90 b = 45.697 β = 90 c = 51.89 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M 2014-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.77 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 0.85 51.89 95.2 0.076 0.091 0.049 13.2 6.2 87934
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.85 0.86 65.2 0.697 0.893 0.55 3.8 3.8
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-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 3rn3 0.85 34.294 85346 4279 92.225 0.113 0.1123 0.1123 0.1291 0.129 7.596
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] 0.173 0.379 -0.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.722 r_dihedral_angle_3_deg 13.537 r_dihedral_angle_4_deg 8.337 r_dihedral_angle_1_deg 7.503 r_lrange_it 5.422 r_rigid_bond_restr 5.284 r_lrange_other 3.251 r_angle_refined_deg 2.474 r_scangle_it 1.726 r_angle_other_deg 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.722 r_dihedral_angle_3_deg 13.537 r_dihedral_angle_4_deg 8.337 r_dihedral_angle_1_deg 7.503 r_lrange_it 5.422 r_rigid_bond_restr 5.284 r_lrange_other 3.251 r_angle_refined_deg 2.474 r_scangle_it 1.726 r_angle_other_deg 1.68 r_scbond_it 1.582 r_scbond_other 1.45 r_scangle_other 1.348 r_mcangle_it 1.255 r_mcangle_other 1.254 r_mcbond_it 0.926 r_mcbond_other 0.922 r_symmetry_nbd_refined 0.383 r_symmetry_xyhbond_nbd_refined 0.352 r_nbd_other 0.344 r_xyhbond_nbd_refined 0.331 r_symmetry_xyhbond_nbd_other 0.301 r_nbd_refined 0.263 r_symmetry_nbd_other 0.222 r_nbtor_refined 0.189 r_chiral_restr 0.127 r_symmetry_nbtor_other 0.107 r_bond_refined_d 0.02 r_gen_planes_refined 0.017 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 951 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction xia2 data scaling MOLREP phasing