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Crystal Structure of Intracellular Chorismate Mutase from Mycobacterium Tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YBZ pdb entry 1YBZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.6 295 20% polyethylene glycol 400, 0.1M tris pH 8.6, 0.2M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.11 41.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.86 α = 90 b = 59.86 β = 90 c = 47.52 γ = 90
Symmetry Space Group P 43 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 RIGAKU RAXIS IV++ msc blue confocal 2007-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 19.33 100 0.056 25.3 14.7 6192
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 2.07 100 0.323 7 14.8 594
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 1YBZ 2 19.33 6191 295 99.92 0.222 0.219 0.2255 0.298 0.308 RANDOM 42.997
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] -2.01 -2.01 4.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.22 r_dihedral_angle_4_deg 21.145 r_dihedral_angle_3_deg 19.515 r_dihedral_angle_1_deg 5.655 r_scangle_it 5.232 r_scbond_it 3.198 r_mcangle_it 2.045 r_angle_refined_deg 1.985 r_mcbond_it 1.306 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.22 r_dihedral_angle_4_deg 21.145 r_dihedral_angle_3_deg 19.515 r_dihedral_angle_1_deg 5.655 r_scangle_it 5.232 r_scbond_it 3.198 r_mcangle_it 2.045 r_angle_refined_deg 1.985 r_mcbond_it 1.306 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.25 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.206 r_symmetry_hbond_refined 0.163 r_chiral_restr 0.119 r_bond_refined_d 0.021 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 573 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction