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Ribonuclease A- uridine 5' phosphate 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 5.5 289 PEG 4000, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.13 42.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.035 α = 90 b = 32.299 β = 90.91 c = 72.475 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 MAR CCD 165 mm 2007-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.0448 SRS PX10.1
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 1.39 30 94.7 0.106 34.5 2.6 44340 42114 -3 16.008
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) 1.39 1.42 91.5 0.263 4.1 2.6 3122
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 1.39 30 42114 42114 2225 94.74 0.2101 0.20779 0.206 0.25398 0.2519 RANDOM 21.914
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] -0.05 0.42 0.23 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.208 r_dihedral_angle_3_deg 11.538 r_dihedral_angle_4_deg 10.652 r_dihedral_angle_1_deg 5.847 r_sphericity_free 4.105 r_sphericity_bonded 3.934 r_scangle_it 3.371 r_scbond_it 2.515 r_rigid_bond_restr 1.758 r_mcangle_it 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.208 r_dihedral_angle_3_deg 11.538 r_dihedral_angle_4_deg 10.652 r_dihedral_angle_1_deg 5.847 r_sphericity_free 4.105 r_sphericity_bonded 3.934 r_scangle_it 3.371 r_scbond_it 2.515 r_rigid_bond_restr 1.758 r_mcangle_it 1.72 r_angle_refined_deg 1.403 r_mcbond_it 1.139 r_nbtor_refined 0.297 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.177 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1907 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling REFMAC phasing