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Crystal structure of the co-expressed succinyl-CoA transferase A and B complex from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M3E PDB entry 1M3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 289 0.1M tri-Sodium citrate dihydrate pH 5.6, 20% Isopropanol, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.33 47.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.337 α = 90 b = 70.404 β = 106.31 c = 97.996 γ = 90
Symmetry Space Group P 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 315 Mirrors 2007-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793 APS 19-ID
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 2.59 48.3 99.7 0.147 0.147 5.9 3.5 28084 28084 -3 47.7
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) 2.59 2.69 94.2 0.543 0.543 2.2 3.2
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 (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 1M3E 2.59 48.3 28069 28069 1417 99.21 0.19564 0.19257 0.193 0.25278 0.2524 RANDOM 53.745
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] -3.03 -0.53 2.07 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.356 r_dihedral_angle_3_deg 22.442 r_dihedral_angle_4_deg 19.168 r_dihedral_angle_1_deg 6.976 r_scangle_it 5.569 r_mcangle_it 4.414 r_scbond_it 3.26 r_mcbond_it 2.598 r_angle_refined_deg 1.599 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.356 r_dihedral_angle_3_deg 22.442 r_dihedral_angle_4_deg 19.168 r_dihedral_angle_1_deg 6.976 r_scangle_it 5.569 r_mcangle_it 4.414 r_scbond_it 3.26 r_mcbond_it 2.598 r_angle_refined_deg 1.599 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.306 r_nbd_refined 0.246 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 6605 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing Coot model building REFMAC refinement SBC-Collect data collection HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling