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Crystal structure of enoyl-CoA hydratase EchA1 from Mycobacterium marinum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IEX PDB ENTRY 2IEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 MymaA.01530.f.A1 PS00846 at 33.15 mg/mL against JCSG+ A5, 0.2 M magnesium formate, 25% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 218651a5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.17 43.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.78 α = 90 b = 77.71 β = 107.94 c = 76.47 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 CCD ADSC QUANTUM 315r 2010-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 2.2 50 96.9 0.08 14.4 3.7 36052 34932 -3 30.815
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 2.2 2.26 82 0.412 2.83 3.3 2672
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 2IEX 2.2 50 34879 1735 96.86 0.1768 0.1736 0.177 0.237 0.2365 RANDOM 25.579
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] 1.82 0.2 0.28 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.33 r_dihedral_angle_4_deg 20.629 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_1_deg 5.675 r_scangle_it 3.505 r_scbond_it 2.072 r_angle_refined_deg 1.441 r_mcangle_it 1.181 r_mcbond_it 0.652 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.33 r_dihedral_angle_4_deg 20.629 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_1_deg 5.675 r_scangle_it 3.505 r_scbond_it 2.072 r_angle_refined_deg 1.441 r_mcangle_it 1.181 r_mcbond_it 0.652 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5332 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction