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Crystal structure of Dihydrodipicolinate Synthase from Mycobacterium tuberculosis in complex with alpha-ketopimelic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 1.34M tri-sodium citrate, 0.1M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.44 49.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.78 α = 90 b = 84.78 β = 90 c = 83.92 γ = 90
Symmetry Space Group P 42 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 100 IMAGE PLATE MARRESEARCH 2013-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.4 55 98.8 0.106 0.106 0.114 0.043 13.7 6.8 12296 12296 28.53
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 2.4 2.53 97.3 0.42 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1XXX 2.4 48.781 1.34 12276 593 98.38 0.1981 0.1954 0.1955 0.2512 0.2517 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.072 f_angle_d 0.681 f_chiral_restr 0.043 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2133 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement MOSFLM data collection SCALA data scaling PHASER phasing PDB_EXTRACT data extraction