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high resolution crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (reduced form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TRX modified version of 2TRX (see publication)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277.15 0.1M ammonium acetate, 0.2M sodium acetate, 0.1M sodium iodide, 40% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 1.61 28.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.355 α = 90 b = 46.082 β = 90 c = 74.143 γ = 90
Symmetry Space Group P 21 21 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 CCD MARRESEARCH dynamically bendable mirror 2003-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 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 1.3 20 98.2 0.091 20.8 5.4 25864 -3 12.4
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) 1.3 1.35 87 0.288 3.1 2253
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-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT modified version of 2TRX (see publication) 1.3 15 25054 25027 778 0.17 0.1657 0.198 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 23 0.5 1122.07
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.071 s_zero_chiral_vol 0.066 s_approx_iso_adps 0.057 s_similar_adp_cmpnt 0.052 s_from_restr_planes 0.0271 s_angle_d 0.026 s_anti_bump_dis_restr 0.017 s_bond_d 0.011 s_similar_dist s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1015 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 13
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing