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Catalytic domain of E. coli RNase E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BX2 PDB ENTRY 2BX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 CRYSTALLIZATION CONDITIONS: CRYSTALS OF THE RNASE E CATALYTIC DOMAIN/ RNA COMPLEX APPEARED AFTER TWO TO FOUR WEEKS IN 5 TO 20 % WT/V POLYETHYLENE GLYCOL 8,000, 0.1 M TRIS PH 7.5 TO 8.0, AND 10 TO 50 MM MAGNESIUM FORMATE AT 20OC
Crystal Properties Matthews coefficient Solvent content 7.1 82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.586 α = 90 b = 196.586 β = 90 c = 140.766 γ = 120
Symmetry Space Group P 62 2 2
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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS ALS
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 3.6 25 99.8 0.13 23 16 19065
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.6 3.73 97.7 0.64 209 10
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 PDB ENTRY 2BX2 3.6 25 17938 973 99.7 0.32 0.319 0.2376 0.347 0.2668 RANDOM 59.1
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] 4.22 2.11 4.22 -6.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.726 r_dihedral_angle_3_deg 28.266 r_dihedral_angle_4_deg 24.522 r_dihedral_angle_1_deg 14.245 r_mcangle_it 5.494 r_scangle_it 5.401 r_scbond_it 3.373 r_mcbond_it 3.211 r_angle_refined_deg 1.975 r_symmetry_vdw_refined 0.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.726 r_dihedral_angle_3_deg 28.266 r_dihedral_angle_4_deg 24.522 r_dihedral_angle_1_deg 14.245 r_mcangle_it 5.494 r_scangle_it 5.401 r_scbond_it 3.373 r_mcbond_it 3.211 r_angle_refined_deg 1.975 r_symmetry_vdw_refined 0.657 r_nbd_refined 0.406 r_nbtor_refined 0.377 r_xyhbond_nbd_refined 0.359 r_symmetry_hbond_refined 0.354 r_chiral_restr 0.118 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3557 Nucleic Acid Atoms 212 Solvent Atoms 6 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling