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Crystal structure of ribonuclease Sa2 with exo-2',3'-cyclophosphorotioate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PY3 PDB entry 1py3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 ammonium sulfate, phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.89 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.221 α = 90 b = 66.775 β = 100.8 c = 57.07 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 100 AREA DETECTOR MARRESEARCH mirrors 2001-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 1.1 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 2.2 20 90.2 0.055 18 3.2 19754 19754 2 2 38.5
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 2.2 2.257 65.4 0.212 4.7 2.9 579
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1py3 2.2 19.94 19754 16896 913 93.24 0.2103 0.2103 0.20756 0.2123 0.26237 0.2678 RANDOM 19.761
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] -1.07 -0.04 2.56 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.865 r_dihedral_angle_4_deg 25.711 r_dihedral_angle_3_deg 16.304 r_dihedral_angle_1_deg 6.623 r_scangle_it 2.434 r_angle_other_deg 1.707 r_scbond_it 1.607 r_angle_refined_deg 1.555 r_mcangle_it 0.953 r_mcbond_it 0.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.865 r_dihedral_angle_4_deg 25.711 r_dihedral_angle_3_deg 16.304 r_dihedral_angle_1_deg 6.623 r_scangle_it 2.434 r_angle_other_deg 1.707 r_scbond_it 1.607 r_angle_refined_deg 1.555 r_mcangle_it 0.953 r_mcbond_it 0.805 r_symmetry_vdw_other 0.239 r_nbd_other 0.219 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.179 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.144 r_mcbond_other 0.13 r_nbtor_other 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2233 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing