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Crystal structure of ribonuclease Sa2 with guanosine-2'-cyclophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 2.94 58.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.489 α = 90 b = 67.313 β = 100.63 c = 57.234 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 2003-06-15 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 1.8 20 98.9 0.054 19.3 35195 34762 2 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 1.82 96.8 0.317 2.7 1104
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 (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 1py3 1.8 20 34762 33012 1750 98.78 0.21707 0.21548 0.2207 0.24635 0.2537 RANDOM 23.922
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] -1.11 0.16 2.28 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.785 r_dihedral_angle_4_deg 20.416 r_dihedral_angle_3_deg 15.922 r_dihedral_angle_1_deg 6.661 r_scangle_it 2.389 r_scbond_it 1.667 r_angle_refined_deg 1.388 r_mcangle_it 0.986 r_angle_other_deg 0.931 r_mcbond_it 0.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.785 r_dihedral_angle_4_deg 20.416 r_dihedral_angle_3_deg 15.922 r_dihedral_angle_1_deg 6.661 r_scangle_it 2.389 r_scbond_it 1.667 r_angle_refined_deg 1.388 r_mcangle_it 0.986 r_angle_other_deg 0.931 r_mcbond_it 0.809 r_nbd_refined 0.21 r_nbd_other 0.21 r_symmetry_vdw_other 0.204 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.178 r_mcbond_other 0.176 r_symmetry_vdw_refined 0.162 r_chiral_restr 0.08 r_nbtor_other 0.079 r_bond_refined_d 0.012 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 2217 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing