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Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase domain from Mycobacterium tuberculosis with sulfate and zinc at pH 4.00
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 4 293 0.1M Na Acetate, 15% PEG 4000, 0.4M ammonium sulfate, pH 4.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.442 α = 90 b = 65.442 β = 90 c = 87.74 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 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2010-02-25 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) 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 2.06 50 98.7 0.047 0.047 48.7 7.3 13240 13240 -3 34.1
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 2.06 2.13 87.2 0.293 0.293 5.7 5 1140
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 2.06 34.69 13031 12393 638 99.16 0.19376 0.19171 0.1892 0.2358 0.2306 RANDOM 35.694
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] 0.99 0.49 0.99 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.502 r_dihedral_angle_4_deg 19.657 r_dihedral_angle_3_deg 18.365 r_dihedral_angle_1_deg 5.882 r_scangle_it 3.998 r_scbond_it 2.34 r_mcangle_it 1.816 r_angle_refined_deg 1.433 r_mcbond_it 0.98 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.502 r_dihedral_angle_4_deg 19.657 r_dihedral_angle_3_deg 18.365 r_dihedral_angle_1_deg 5.882 r_scangle_it 3.998 r_scbond_it 2.34 r_mcangle_it 1.816 r_angle_refined_deg 1.433 r_mcbond_it 0.98 r_chiral_restr 0.104 r_bond_refined_d 0.013 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 1427 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 17
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling