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Crystal structure of Enoyl-CoA hydratase EchA8_6 from Mycobacterium marinum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FDU PDB ENTRY 3FDU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 290 Internal tracking number 218458A5. JCSG screen condition A5:
20% PEG3350, 0.2 M Magnesium formate. MymaA.00358.c.A1 PS00818 at 69.82 mg/ml., pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.41 48.906
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.82 α = 90 b = 115.82 β = 90 c = 115.82 γ = 90
Symmetry Space Group I 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+ 2011-02-03 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 2.2 33.43 99.5 0.074 23.62 7.8 13294 13222 -3 37.348
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 96.7 0.461 5.8 7.1 972
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 MR THROUGHOUT PDB ENTRY 3FDU 2.2 33.43 13166 650 99.23 0.185 0.183 0.1976 0.217 0.235 RANDOM 31.051
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 35.505 r_dihedral_angle_4_deg 20.292 r_dihedral_angle_3_deg 11.396 r_dihedral_angle_1_deg 6.058 r_scangle_it 3.324 r_scbond_it 2.022 r_angle_refined_deg 1.328 r_mcangle_it 1.295 r_angle_other_deg 0.955 r_mcbond_it 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.505 r_dihedral_angle_4_deg 20.292 r_dihedral_angle_3_deg 11.396 r_dihedral_angle_1_deg 6.058 r_scangle_it 3.324 r_scbond_it 2.022 r_angle_refined_deg 1.328 r_mcangle_it 1.295 r_angle_other_deg 0.955 r_mcbond_it 0.69 r_mcbond_other 0.14 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1542 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 6
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction