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Crystal structure of an enoyl-coA hydratase EchA12_1 from Mycobacterium marinum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GOW PDB ENTRY 3GOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 39.66 mg/mL MymaA.00305.a.A1 PS00827 against PACT screen condition F10: 0.02 M Na/K phosphate, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 218672f10, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.765866 30.345789
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.7 α = 90 b = 87.7 β = 90 c = 87.7 γ = 90
Symmetry Space Group P 21 3
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+ 2011-01-31 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 2.4 50 99.9 0.063 24.74 7.1 9052 9040 -3 46.082
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 2.4 2.46 100 0.519 4.33 7.1 667
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 3GOW 2.4 50 9002 471 99.45 0.1821 0.1796 0.1796 0.229 0.1968 RANDOM 36.3734
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 r_dihedral_angle_2_deg 32.43 r_dihedral_angle_4_deg 15.943 r_dihedral_angle_3_deg 13.999 r_dihedral_angle_1_deg 5.679 r_scangle_it 3.251 r_scbond_it 1.996 r_angle_refined_deg 1.323 r_mcangle_it 1.157 r_mcbond_it 0.622 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.43 r_dihedral_angle_4_deg 15.943 r_dihedral_angle_3_deg 13.999 r_dihedral_angle_1_deg 5.679 r_scangle_it 3.251 r_scbond_it 1.996 r_angle_refined_deg 1.323 r_mcangle_it 1.157 r_mcbond_it 0.622 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1443 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 2
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction