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Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase (triclinic form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XT9 PDB ENTRY 2XT9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 46.5% MPD, 100 MM HEPES, PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.74 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.539 α = 99.48 b = 83.244 β = 99.06 c = 158.61 γ = 101.25
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 CCD TOROIDAL FOCUSING MIRROR 2009-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.96 49.5 95.2 0.09 8.7 2.9 263780 2 23.55
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 1.96 2.07 91.5 0.44 2.2 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 2XT9 1.96 39.2 263738 13228 95.19 0.1896 0.1884 0.2068 0.2108 0.2339 RANDOM 28.82
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] -2.9185 -0.2784 1.1846 0.3211 0.8939 2.5975
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.47 t_other_torsion 2.63 t_angle_deg 0.98 t_bond_d 0.01 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_omega_torsion 3.47 t_other_torsion 2.63 t_angle_deg 0.98 t_bond_d 0.01 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 25015 Nucleic Acid Atoms Solvent Atoms 1221 Heterogen Atoms 112
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling MOLREP phasing