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Crystal structure of an enoyl-CoA hydratase (ECHA3) from Mycobacterium marinum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OT6 PDB entry 3OT6 modified with CCP4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 EBS JCSG+ SCREEN D12: 40mM potassium dihydrogen phosphate, 16% PEG 8000, 20 % glycerol; MYMAA.00829.A.A1 PW29951 AT 20.5MG/ML, PH N/A, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.33 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.21 α = 90 b = 77.21 β = 90 c = 66.11 γ = 120
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 HF 2010-02-21 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) R Sym 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 1.75 50 99.9 0.042 0.042 34.8 8.4 22672 22658 15.9
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 1.75 1.8 99.9 0.325 4.8 4.7 1658
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3OT6 modified with CCP4 program chainsaw 1.75 50 22658 22634 1157 99.8 0.144 0.144 0.142 0.15 0.178 0.1818 RANDOM 12.18
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] 0.3 0.15 0.3 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_dihedral_angle_4_deg 18.688 r_dihedral_angle_3_deg 11.684 r_dihedral_angle_1_deg 5.296 r_scangle_it 3.653 r_scbond_it 2.181 r_angle_refined_deg 1.356 r_mcangle_it 1.325 r_angle_other_deg 0.962 r_mcbond_it 0.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_dihedral_angle_4_deg 18.688 r_dihedral_angle_3_deg 11.684 r_dihedral_angle_1_deg 5.296 r_scangle_it 3.653 r_scbond_it 2.181 r_angle_refined_deg 1.356 r_mcangle_it 1.325 r_angle_other_deg 0.962 r_mcbond_it 0.767 r_mcbond_other 0.223 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1640 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling