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Ribonuclease A uridine 5' diphosphate 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 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.003 α = 90 b = 32.337 β = 90.72 c = 72.299 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 1.4 30 97.7 0.044 29 2.9 45026 42757 -3 14.5
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) 1.4 1.42 100 0.111 8.2 2.9 2290
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 1.4 30 45026 42757 2266 97.72 0.18976 0.18791 0.1861 0.22497 0.2213 RANDOM 19.566
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] -0.35 0.04 0.34 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.334 r_dihedral_angle_3_deg 11.537 r_dihedral_angle_4_deg 7.989 r_dihedral_angle_1_deg 5.904 r_sphericity_free 4.409 r_sphericity_bonded 4.167 r_scangle_it 3.44 r_scbond_it 2.407 r_mcangle_it 1.787 r_angle_refined_deg 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.334 r_dihedral_angle_3_deg 11.537 r_dihedral_angle_4_deg 7.989 r_dihedral_angle_1_deg 5.904 r_sphericity_free 4.409 r_sphericity_bonded 4.167 r_scangle_it 3.44 r_scbond_it 2.407 r_mcangle_it 1.787 r_angle_refined_deg 1.41 r_rigid_bond_restr 1.381 r_mcbond_it 1.149 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.234 r_symmetry_hbond_refined 0.2 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1910 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling REFMAC phasing