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atomic resolution crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (reduced form at pH7)
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 1.7 28.110168
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.289 α = 90 b = 46.072 β = 90 c = 74.07 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 101 CCD MARRESEARCH dynamically bendable mirror 2004-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.8555 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 0.99 20 99.6 0.079 18.8 5.8 58388 -3 6.196
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) 0.99 1.03 96.9 0.445 2.6
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 modified version of 2TRX (see publication) 0.99 15 56874 56874 1437 0.113 0.146 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 60 901.7 1107.68
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.089 s_zero_chiral_vol 0.08 s_approx_iso_adps 0.078 s_similar_adp_cmpnt 0.045 s_anti_bump_dis_restr 0.039 s_angle_d 0.03 s_from_restr_planes 0.0264 s_bond_d 0.014 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1108 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 3
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing