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Crystal structure of the disulfide-linked complex between the N-terminal and C-terminal domain of the electron transfer catalyst DsbD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JZD PDB ENTRY 1JZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 sodium acetate, sodium formate, PEG 2000 MME, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.82 56.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.46 α = 90 b = 52.6 β = 100.39 c = 107.92 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 98.2 CCD MARRESEARCH Dynamically bendable mirror 2003-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.751 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.85 20 99.3 0.08 16.1 4.4 24676 24336 -3 68.8
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 2.85 2.95 97.3 0.362 3.6 3.3 2376
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JZD 2.85 20 24676 24336 707 0.224 0.284 RANDOM 38.4
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] -6.058 2.138 2.236 3.822
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.16 c_scangle_it 3.643 c_mcangle_it 2.503 c_scbond_it 2.315 c_mcbond_it 1.474 c_angle_deg 1.24 c_improper_angle_d 0.83 c_bond_d 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5670 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement