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Crystal structure of Mycobacterium smegmatis alpha-ketoglutarate decarboxylase homodimer (orthorhombic 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 39% MPD, 100 MM HEPES, PH 7.0, 200 MM NACL
Crystal Properties Matthews coefficient Solvent content 3.3 62.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.99 α = 90 b = 247.72 β = 90 c = 79.98 γ = 90
Symmetry Space Group P 21 21 2
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 2009-09-26 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 2.74 82 99.3 0.07 10.3 3.5 79835 2.4 75.02
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 2.74 2.89 97.5 0.42 2.4 3.2
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 2.74 40.12 79534 4017 99.13 0.1874 0.1854 0.1927 0.2236 0.2315 RANDOM 70.04
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] 25.4159 -9.113 -16.303
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.11 t_other_torsion 2.95 t_angle_deg 1.09 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 3.11 t_other_torsion 2.95 t_angle_deg 1.09 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 15727 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 56
Software Software Software Name Purpose BUSTER-TNT refinement MOSFLM data reduction SCALA data scaling MOLREP phasing