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Crystal structure of enoyl-CoA hydratase EchA5 from Mycobacterium marinum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H81 PDB ENTRY 3H81
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 Crystal tracking ID 218457h19. JCSG+ screen condition H10: 0.2 M ammonium acetate, 0.1 M Bis-Tris propane, 25% PEG3350, 46.3 mg/mL MymaA.00386.a.A1 PS00820, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.12 41.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.04 α = 90 b = 118.92 β = 90 c = 132.48 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 CCD RIGAKU SATURN 944+ VariMax 2011-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
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 2.15 50 97.4 0.092 11.08 4 75404 73428 -3 31.017
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 2.15 2.21 90.7 0.461 2.44 2.6 5531
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 PDB ENTRY 3H81 2.15 50 73236 3698 97.13 0.1706 0.1683 0.1755 0.2134 0.2214 RANDOM 24.4438
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] -1.34 0.71 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.912 r_dihedral_angle_4_deg 18.456 r_dihedral_angle_3_deg 12.948 r_dihedral_angle_1_deg 5.868 r_scangle_it 3.299 r_scbond_it 2.106 r_angle_refined_deg 1.411 r_mcangle_it 1.148 r_mcbond_it 0.63 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.912 r_dihedral_angle_4_deg 18.456 r_dihedral_angle_3_deg 12.948 r_dihedral_angle_1_deg 5.868 r_scangle_it 3.299 r_scbond_it 2.106 r_angle_refined_deg 1.411 r_mcangle_it 1.148 r_mcbond_it 0.63 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10339 Nucleic Acid Atoms Solvent Atoms 672 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction