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Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase in complex with the enamine-ThDP intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YIC PDB ENTRY 2YIC
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 2.71 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.843 α = 99.23 b = 82.287 β = 99.03 c = 163.478 γ = 100.63
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 2.25 41.9 95.7 0.1 6.9 2 179918 2 30.43
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 2.25 2.37 94.6 0.48 2 1.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2YIC 2.25 32.94 179896 9062 95.71 0.1935 0.192 0.2234 0.2301 RANDOM 33.53
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] -0.8828 1.1116 -0.4018 4.5879 0.5883 -3.7051
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.22 t_other_torsion 2.83 t_angle_deg 1.01 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 3.22 t_other_torsion 2.83 t_angle_deg 1.01 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 26102 Nucleic Acid Atoms Solvent Atoms 730 Heterogen Atoms 140
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling MOLREP phasing