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The RNase A- 5'-Deoxy-5'-N-(ethyl isonipecotatyl)uridine 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 2.19 43.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.384 α = 90 b = 32.876 β = 90.4 c = 72.621 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 Merge 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 1.58 30 94.9 0.057 16.5 7.3 31270 31074 -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 1.58 1.62 96.6 0.274 3.8 2.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 2G8Q 1.58 30 29500 1574 94.48 0.18793 0.18592 0.183 0.22678 0.2223 RANDOM 15.397
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] -0.12 -0.1 -0.35 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.563 r_dihedral_angle_4_deg 12.304 r_dihedral_angle_3_deg 10.926 r_dihedral_angle_1_deg 5.76 r_scangle_it 2.053 r_scbond_it 1.299 r_angle_refined_deg 1.155 r_mcangle_it 0.882 r_mcbond_it 0.546 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.563 r_dihedral_angle_4_deg 12.304 r_dihedral_angle_3_deg 10.926 r_dihedral_angle_1_deg 5.76 r_scangle_it 2.053 r_scbond_it 1.299 r_angle_refined_deg 1.155 r_mcangle_it 0.882 r_mcbond_it 0.546 r_nbtor_refined 0.294 r_symmetry_vdw_refined 0.189 r_nbd_refined 0.182 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.074 r_bond_refined_d 0.009 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 313 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling REFMAC phasing