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Crystal structure of a glutaryl-coa dehydrogenase from mycobacterium smegmatis in complex with FADH2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EBA PDB entry 2eba modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 20% PEG 3350, 200MM POTASSIUM CITRATE TRIBASIC; MYSMA.01640.BA1, PW28880 AT 30.7 MG/ML; ADD 15% EG TO RESERVOIR FOR CRYO, PH N/A, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.67 α = 90 b = 66.87 β = 107.71 c = 167.46 γ = 90
Symmetry Space Group C 1 2 1
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 315r 2011-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
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 1.45 50 99.3 0.039 0.039 21.69 3.6 278810 276750 -3 18.25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.49 93.9 0.309 0.309 3.2 2.5 20619
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 2eba modified with CCP4 program CHAINSAW 1.45 45.48 278810 276456 13939 99.2 0.128 0.128 0.127 0.1361 0.15 0.1585 RANDOM 9.35
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] -0.29 -0.01 0.54 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.388 r_dihedral_angle_4_deg 17.402 r_dihedral_angle_3_deg 11.542 r_dihedral_angle_1_deg 5.317 r_scangle_it 3.378 r_scbond_it 2.121 r_angle_refined_deg 1.51 r_mcangle_it 1.288 r_angle_other_deg 0.95 r_mcbond_it 0.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.388 r_dihedral_angle_4_deg 17.402 r_dihedral_angle_3_deg 11.542 r_dihedral_angle_1_deg 5.317 r_scangle_it 3.378 r_scbond_it 2.121 r_angle_refined_deg 1.51 r_mcangle_it 1.288 r_angle_other_deg 0.95 r_mcbond_it 0.761 r_mcbond_other 0.244 r_chiral_restr 0.095 r_bond_refined_d 0.014 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 11757 Nucleic Acid Atoms Solvent Atoms 2097 Heterogen Atoms 267
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling