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The crystal structure of the reduced disulphide bond isomerase, DsbC, from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EEJ PDB entry 1EEJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.4 293 0.2 M LiSO4, 0.1 M Tris pH 8.4 and 20% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.897 α = 90 b = 145.799 β = 90 c = 73.582 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 1998-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.906 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 17 100 0.081 0.081 14 11 8103 7953 42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.54 100 0.386 0.386 2.6 5 435
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1EEJ 2.5 16.74 8103 7953 150 100 0.2043 0.2043 0.2031 0.2106 0.26964 0.2578 RANDOM 35.045
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] 0.38 0.59 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.801 r_scangle_it 3.28 r_scbond_it 2.094 r_angle_refined_deg 1.271 r_mcangle_it 1.213 r_mcbond_it 0.619 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.801 r_scangle_it 3.28 r_scbond_it 2.094 r_angle_refined_deg 1.271 r_mcangle_it 1.213 r_mcbond_it 0.619 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.119 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1643 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing