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Crystal structure of enoyl-coa hydratase from mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NJB pdb entry 3NJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 MD PACT SCEEN H12: 200MM NAMALONATE, 100M BISTRISPROPANE, 20% PEG 3350; protein at 27MG/ML, CRYO: 15% EDO, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.04 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.01 α = 90 b = 171.01 β = 90 c = 171.01 γ = 90
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+ 2009-05-05 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) 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 99.6 0.053 20.1 4.8 83314 83011 -3 16.1
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 98.3 0.457 2.1 2.3 5999
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3NJB 1.75 42.75 82903 82903 4087 99.5 0.145 0.145 0.144 0.165 0.15 RANDOM 13.01
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 38.613 r_dihedral_angle_4_deg 12.73 r_dihedral_angle_3_deg 11.27 r_dihedral_angle_1_deg 5.325 r_scangle_it 3.711 r_scbond_it 2.402 r_angle_refined_deg 1.506 r_mcangle_it 1.502 r_angle_other_deg 0.996 r_mcbond_it 0.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.613 r_dihedral_angle_4_deg 12.73 r_dihedral_angle_3_deg 11.27 r_dihedral_angle_1_deg 5.325 r_scangle_it 3.711 r_scbond_it 2.402 r_angle_refined_deg 1.506 r_mcangle_it 1.502 r_angle_other_deg 0.996 r_mcbond_it 0.875 r_mcbond_other 0.288 r_chiral_restr 0.099 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 4367 Nucleic Acid Atoms Solvent Atoms 641 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling