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Structure of Citrate Synthase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E6Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 Citrate synthase crystals grew at 20 degrees Celsius in 0.2M Magnesium chloride hexahydrate, 0.1M Tris pH=8.5, 3.4M 1,6-Hexandiol in a 75/25 protein/reservoir-ratio drop of 1 microlitre and with a protein concentration of 5.2 mg/ml.
Crystal Properties Matthews coefficient Solvent content 2.03 39.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.767 α = 90 b = 148.767 β = 90 c = 182.797 γ = 120
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-F 2012-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9725 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 47.14 99.92 7.91 6.2 24114
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 4E6Y 2.6 47.14 22819 1290 99.04 0.17494 0.17378 0.1728 0.19405 0.2001 RANDOM 54.367
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] 14.13 14.13 -28.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.094 r_dihedral_angle_4_deg 17.827 r_dihedral_angle_3_deg 17.177 r_long_range_B_other 9.502 r_long_range_B_refined 9.5 r_dihedral_angle_1_deg 8.661 r_mcangle_it 5.518 r_mcangle_other 5.516 r_scangle_other 5.435 r_mcbond_it 3.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.094 r_dihedral_angle_4_deg 17.827 r_dihedral_angle_3_deg 17.177 r_long_range_B_other 9.502 r_long_range_B_refined 9.5 r_dihedral_angle_1_deg 8.661 r_mcangle_it 5.518 r_mcangle_other 5.516 r_scangle_other 5.435 r_mcbond_it 3.764 r_mcbond_other 3.754 r_scbond_other 3.594 r_scbond_it 3.593 r_angle_refined_deg 1.757 r_angle_other_deg 0.902 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2966 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement