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1.95 Angstrom Resolution Crystal Structure of DsbA Disulfide Interchange Protein from Klebsiella pneumoniae.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OCF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 Protein: 9.6mg/ml, 0.01M Tris-HCl pH 8.3;
Screen: PEGs II (B9), 0.1M Tris-HCl pH 8.5, 30% (v/v) PEG 400.
Crystal Properties Matthews coefficient Solvent content 2.15 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.401 α = 90.27 b = 42.392 β = 89.78 c = 103.949 γ = 96
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 MARMOSAIC 300 mm CCD C(111) 2018-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.95 30 97.8 0.135 0.135 0.154 0.073 16.8 4.4 51946 -3 18.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 96.3 0.786 0.786 0.897 0.43 0.726 2.7 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4OCF 1.95 27.01 48932 2397 96.41 0.18213 0.17973 0.2084 0.22982 0.2589 RANDOM 22.852
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] -0.36 12.88 0.65 3.66 -13.9 -3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.586 r_dihedral_angle_3_deg 9.702 r_dihedral_angle_4_deg 8.881 r_long_range_B_refined 4.329 r_long_range_B_other 4.232 r_dihedral_angle_1_deg 2.712 r_mcangle_it 2.599 r_mcangle_other 2.598 r_scangle_other 2.387 r_mcbond_it 1.671
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.586 r_dihedral_angle_3_deg 9.702 r_dihedral_angle_4_deg 8.881 r_long_range_B_refined 4.329 r_long_range_B_other 4.232 r_dihedral_angle_1_deg 2.712 r_mcangle_it 2.599 r_mcangle_other 2.598 r_scangle_other 2.387 r_mcbond_it 1.671 r_mcbond_other 1.67 r_scbond_it 1.625 r_scbond_other 1.624 r_angle_refined_deg 1.133 r_angle_other_deg 0.427 r_chiral_restr 0.056 r_gen_planes_refined 0.038 r_gen_planes_other 0.034 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6032 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MrBUMP phasing