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RNase A- 5'-Deoxy-5'-N-piperidinothymidine 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 2.15 42.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.161 α = 90 b = 32.421 β = 90.9 c = 72.567 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 1.72 30 97.9 0.078 9.2 10.8 25226 24530 -3 19.5
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 1.7 1.76 96.7 0.47 3 3.1 1218
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 2G8Q 1.72 30 23272 1258 97.24 0.19137 0.18926 0.2296 0.3023 RANDOM 16.746
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] -0.39 0.17 0.73 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_3_deg 11.593 r_dihedral_angle_4_deg 10.506 r_dihedral_angle_1_deg 5.862 r_scangle_it 2.498 r_scbond_it 1.572 r_angle_refined_deg 1.204 r_mcangle_it 0.948 r_mcbond_it 0.553 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_3_deg 11.593 r_dihedral_angle_4_deg 10.506 r_dihedral_angle_1_deg 5.862 r_scangle_it 2.498 r_scbond_it 1.572 r_angle_refined_deg 1.204 r_mcangle_it 0.948 r_mcbond_it 0.553 r_nbtor_refined 0.292 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.184 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1901 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling REFMAC phasing