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Crystal Structure of DNase I Domain of Ribonuclease E from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VRT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 Protein: 7.9 mg/ml, 0.01M Tris pH 8.3;
Screen: PACT (F3), 0.2M Sodium iodide, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.614 α = 90 b = 58.812 β = 108.16 c = 47.046 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 300 mm CCD Be 2020-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.85 30 99.4 0.088 0.088 0.097 0.041 0.985 21.9 5.7 17863 -3 34.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 0.759 0.759 0.833 0.339 0.927 4.7 6
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 MOLECULAR REPLACEMENT THROUGHOUT 2vrt 1.85 29.41 16959 887 98.9 0.2085 0.2067 0.2139 0.2429 0.247 RANDOM 43.735
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] 2.65 1.64 -1.57 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.204 r_dihedral_angle_4_deg 10.434 r_dihedral_angle_3_deg 9.084 r_dihedral_angle_1_deg 2.049 r_angle_refined_deg 1.292 r_angle_other_deg 0.41 r_chiral_restr 0.057 r_gen_planes_refined 0.05 r_gen_planes_other 0.044 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.204 r_dihedral_angle_4_deg 10.434 r_dihedral_angle_3_deg 9.084 r_dihedral_angle_1_deg 2.049 r_angle_refined_deg 1.292 r_angle_other_deg 0.41 r_chiral_restr 0.057 r_gen_planes_refined 0.05 r_gen_planes_other 0.044 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1709 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing