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Crystal structure of glutaryl-CoA dehydrogenase from Burkholderia pseudomallei with fragment (1,4-dimethyl-1,2,3,4-tetrahydroquinoxalin-6-yl)methylamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D6B PDB entry 3D6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 20% PEG 3000, 0.1M HEPES pH 7.5, 0.2M NaCl. Soaked overnight with 25 mM (1,4-dimethyl-1,2,3,4-tetrahydroquinoxalin-6-yl)methylamine, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.16 42.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.418 α = 90 b = 106.374 β = 90 c = 144.774 γ = 90
Symmetry Space Group P 21 21 21
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 315 2009-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97 ALS 5.0.3
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 1.99 50 100 0.073 10.1 7.2 103621
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 1.99 2.06 100 0.686 6.1
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 3D6B 1.99 50 103473 5175 0.202 0.2 0.1976 0.238 0.2367 RANDOM 38.32
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] 0.52 -0.45 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.916 r_dihedral_angle_4_deg 20.856 r_dihedral_angle_3_deg 14.48 r_dihedral_angle_1_deg 5.572 r_scangle_it 3.801 r_scbond_it 2.377 r_mcangle_it 1.519 r_angle_refined_deg 1.431 r_mcbond_it 0.84 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.916 r_dihedral_angle_4_deg 20.856 r_dihedral_angle_3_deg 14.48 r_dihedral_angle_1_deg 5.572 r_scangle_it 3.801 r_scbond_it 2.377 r_mcangle_it 1.519 r_angle_refined_deg 1.431 r_mcbond_it 0.84 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11525 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 42
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling