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Crystal Structure of E. coli RNase E Apoprotein - Catalytic Domain
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 8.5 pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.89 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.241 α = 94.95 b = 75.571 β = 102.03 c = 109.37 γ = 91.77
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 2002-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
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 3.22 50 91.4 0.11 11.1 3.7 34917
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 3.22 3.34 67.5 0.46 1.7 2.9
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 3.3 47.84 31611 1664 96.9 0.268 0.267 0.2745 0.293 0.3041 RANDOM 99.52
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] 4.55 -6.28 -1.94 -1.95 0.41 -3.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.638 r_dihedral_angle_3_deg 18.652 r_dihedral_angle_4_deg 18.194 r_dihedral_angle_1_deg 8.595 r_scangle_it 7.42 r_mcangle_it 6 r_scbond_it 4.708 r_mcbond_it 4.204 r_angle_refined_deg 0.95 r_symmetry_vdw_refined 0.557
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.638 r_dihedral_angle_3_deg 18.652 r_dihedral_angle_4_deg 18.194 r_dihedral_angle_1_deg 8.595 r_scangle_it 7.42 r_mcangle_it 6 r_scbond_it 4.708 r_mcbond_it 4.204 r_angle_refined_deg 0.95 r_symmetry_vdw_refined 0.557 r_symmetry_hbond_refined 0.518 r_nbtor_refined 0.318 r_nbd_refined 0.26 r_xyhbond_nbd_refined 0.208 r_chiral_restr 0.111 r_bond_refined_d 0.025 r_gen_planes_refined 0.021 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 14170 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing MOLREP phasing REFMAC phasing