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Crystal structure of Enoyl-[acyl-carrier-protein] reductase [NADH] (InhA) from Mycobacterium kansasii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H7I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 Optimization condition around Microlytic MCSG1 screen, condition F8: 3000mM sodium formate pH 7.0: MykaA.00472.a.B1.PS38576, at 27.1mg/ml: cryo: 20%EG: tray 311486 b1: puck ybk8-4.
Crystal Properties Matthews coefficient Solvent content 3.3 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.98 α = 90 b = 92.98 β = 90 c = 182.62 γ = 90
Symmetry Space Group I 41 2 2
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 RIGAKU SATURN 944+ Rigaku VariMax 2019-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.95 50 99.8 0.045 0.047 1 36.94 12.1 29565 28.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.9 0.544 0.588 0.9 3.53 6.898
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2h7i 1.95 46.49 1.34 29548 1974 99.79 0.1639 0.1619 0.1651 0.193 0.1939 0 33.86
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 10.4871 f_angle_d 0.8211 f_chiral_restr 0.0521 f_bond_d 0.0062 f_plane_restr 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2002 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing Coot model building PHENIX model building