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C-terminal domain of the thiol:disulfide interchange protein DsbD, Q488K mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FWF PDB ENTRY 2FWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 21 mg/mL protein, 20% PEG4000, 0.1 M sodium citrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.107 α = 90 b = 51.53 β = 90 c = 85.039 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2012-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.47 100 89.8 0.132 9.1 4.1 5954 5345 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.56 70 0.433 1.98 1.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 2FWF 2.47 29.013 0.07 5917 5032 230 85.09 0.1962 0.1934 0.1943 0.2551 0.2484 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] -2.5646 -0.8974 -1.4659
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.737 f_angle_d 0.659 f_chiral_restr 0.043 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 944 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing PHENIX refinement DENZO data reduction SCALEPACK data scaling