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Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase in complex with the enamine-ThDP intermediate and acetyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XT7 PDB ENTRY 2XT7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.6 52% MPD, 20 MM SODIUM ACETATE, 5% 1-3-PROPANEDIOL, pH 7.6
Crystal Properties Matthews coefficient Solvent content 2.73 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.062 α = 99.26 b = 81.953 β = 97.09 c = 161.876 γ = 100.58
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC CCD KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS 2010-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 2.4 41.4 95.8 0.1 7.4 2.5 149496 2 41.18
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 2.4 2.53 95.6 0.56 1.9 2.4
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 2XT7 2.4 35.14 149475 7517 95.79 0.198 0.1968 0.2156 0.2202 0.2419 RANDOM 44.81
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] -2.6692 -1.5954 5.2656 -0.0948 -0.0061 2.764
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 2.73 t_omega_torsion 2.66 t_angle_deg 0.97 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 2.73 t_omega_torsion 2.66 t_angle_deg 0.97 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25968 Nucleic Acid Atoms Solvent Atoms 514 Heterogen Atoms 327
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling MOLREP phasing