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The Ribonuclease A- 5'-Deoxy-5'-N-pyrrolidinouridine complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G8Q PDB ENTRY: 2G8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 PEG 4000, SODIUM CITRATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.959 α = 90 b = 32.54 β = 90.62 c = 72.439 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 CCD ADSC QUANTUM 4 2006-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.92 SRS PX9.6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.6 30 96.4 0.051 11.7 3.2 31418 30196 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 95.9 0.174 3 3.3
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY: 2G8Q 1.6 30 31418 28676 1519 96.22 0.18041 0.17868 0.1761 0.2133 0.2102 RANDOM 14.916
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] -0.07 0.05 0.36 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.003 r_dihedral_angle_4_deg 11.107 r_dihedral_angle_3_deg 10.903 r_dihedral_angle_1_deg 5.757 r_scangle_it 2.214 r_angle_refined_deg 1.429 r_scbond_it 1.354 r_mcangle_it 0.808 r_mcbond_it 0.479 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.003 r_dihedral_angle_4_deg 11.107 r_dihedral_angle_3_deg 10.903 r_dihedral_angle_1_deg 5.757 r_scangle_it 2.214 r_angle_refined_deg 1.429 r_scbond_it 1.354 r_mcangle_it 0.808 r_mcbond_it 0.479 r_nbtor_refined 0.292 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.162 r_chiral_restr 0.135 r_symmetry_hbond_refined 0.13 r_xyhbond_nbd_refined 0.124 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling REFMAC phasing