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RNase A- 5'-Deoxy-5'-N-pyrrolidinothymidine 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 2.16 43.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.102 α = 90 b = 32.678 β = 90.51 c = 72.562 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 2006-11-08 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 1.98 30 98.9 0.091 8.7 2.9 16850 16481 -3 21
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 1.98 2.03 100 0.435 2.8 2.9 852
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 1.98 28.6 16850 15649 832 97.82 0.19178 0.18929 0.1888 0.24022 0.242 RANDOM 18.096
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] -0.14 -0.1 0.29 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.959 r_dihedral_angle_3_deg 13.308 r_dihedral_angle_4_deg 13.076 r_dihedral_angle_1_deg 6.39 r_scangle_it 2.5 r_scbond_it 1.602 r_angle_refined_deg 1.58 r_mcangle_it 0.87 r_mcbond_it 0.526 r_nbtor_refined 0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.959 r_dihedral_angle_3_deg 13.308 r_dihedral_angle_4_deg 13.076 r_dihedral_angle_1_deg 6.39 r_scangle_it 2.5 r_scbond_it 1.602 r_angle_refined_deg 1.58 r_mcangle_it 0.87 r_mcbond_it 0.526 r_nbtor_refined 0.291 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.15 r_symmetry_hbond_refined 0.137 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling REFMAC phasing