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Crystal Structure of EcDsbA in a complex with (1-methyl-1H-pyrazol-5-yl)methanamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FVK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293.15 11-13 % PEG 8000, 5-7.5% GLYCEROL, 100MM NA CACODYLATE PH6.1, 1MM CuCl2
Crystal Properties Matthews coefficient Solvent content 2.73 54.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.56 α = 90 b = 65.082 β = 126.282 c = 74.938 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 100 PIXEL DECTRIS EIGER X 16M 2019-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95365 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.47 49.09 99.4 0.049 0.053 0.028 1 13.1 6.9 75786 22.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.49 88.7 1.057 0.661 0.66 0.557 0.9 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1FVK 1.6 34.59 1.39 59109 759 99.93 0.1807 0.1805 0.1805 0.1976 0.1993 29.52
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.534 f_angle_d 0.9782 f_chiral_restr 0.058 f_bond_d 0.0081 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2863 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing