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Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, first post-decarboxylation intermediate from 2-oxoadipate
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 59% MPD, 22.5 MM NA ACETATE PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.63 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.366 α = 99.76 b = 83.8 β = 99.06 c = 159.513 γ = 100.61
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS 2012-04-05 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 2.15 41.82 97.5 0.06 9.8 2.6 209671 39.66
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 2.15 2.27 96.5 0.42 2.3 2.5
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 2YIC 2.15 41.11 209661 10531 97.49 0.2241 0.223 0.2281 0.2457 0.2557 RANDOM 43.94
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] -3.1108 1.9324 -1.5589 -0.0366 0.2256 3.1474
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.33 t_other_torsion 2.68 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 3.33 t_other_torsion 2.68 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 24960 Nucleic Acid Atoms Solvent Atoms 1088 Heterogen Atoms 144
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling MOLREP phasing