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Crystal structure of Glutaryl-COA dehydrogenase from Burkholderia Pseudomallei with fragment 6421
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 7.5 298 20% PEG 3000, 0.1M HEPES, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.239 α = 90 b = 106.104 β = 90 c = 144.239 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 2009-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 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 2.15 50 99.6 0.072 10.8 7 81993
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 2.15 2.19 98.5 0.593 6.8
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 2.15 46.68 81910 4105 0.209 0.206 0.211 0.255 0.2561 RANDOM 37.44
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] 0.14 -0.32 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_dihedral_angle_4_deg 20.251 r_dihedral_angle_3_deg 14.756 r_dihedral_angle_1_deg 5.71 r_scangle_it 2.465 r_scbond_it 1.509 r_angle_refined_deg 1.245 r_mcangle_it 1.095 r_angle_other_deg 0.902 r_mcbond_it 0.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.604 r_dihedral_angle_4_deg 20.251 r_dihedral_angle_3_deg 14.756 r_dihedral_angle_1_deg 5.71 r_scangle_it 2.465 r_scbond_it 1.509 r_angle_refined_deg 1.245 r_mcangle_it 1.095 r_angle_other_deg 0.902 r_mcbond_it 0.593 r_mcbond_other 0.102 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 11546 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 114
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling