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Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase domain from Mycobacterium tuberculosis at pH 6.00
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MGZ PDB ENTRY 3MGZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 20% PEG 3350, 0.1M potassium phosphate(pH 6.00), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.784 α = 90 b = 51.316 β = 112.76 c = 95.407 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD mirrors 2009-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97372 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 50 96.4 0.087 0.087 20 5.9 37031 37031 -3 19.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 78.8 0.363 0.363 3.5 4.8 2886
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3MGZ 1.8 43.99 35669 33871 1798 96.02 0.1872 0.18482 0.1827 0.23349 0.2314 RANDOM 23.18
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] 2.6 0.9 -0.99 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.719 r_dihedral_angle_4_deg 18.604 r_dihedral_angle_3_deg 14.172 r_dihedral_angle_1_deg 5.657 r_scangle_it 3.803 r_scbond_it 2.333 r_mcangle_it 1.504 r_angle_refined_deg 1.437 r_mcbond_it 0.834 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.719 r_dihedral_angle_4_deg 18.604 r_dihedral_angle_3_deg 14.172 r_dihedral_angle_1_deg 5.657 r_scangle_it 3.803 r_scbond_it 2.333 r_mcangle_it 1.504 r_angle_refined_deg 1.437 r_mcbond_it 0.834 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2915 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 53
Software Software Software Name Purpose MARMOSAIC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling