☰ Navigation Tabs
Type II dehydroquinase from Mycobacterium Tuberculosis complexed with 3-dehydroshikimate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DHQ PDB entry 2dhq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 290 MtDHQase protein was concentrated to 10-15 mg/mL prior to crystallization, using Amicon Ultra MWCO 5 KDa protein concentrators. MtDHQase crystals were grown in 4 uL drops composed of 5-7 mg/mL protein incubated with 1.5-fold M excess of ligand, 15% PEG monomethyl ether 2,000, 0.075 M KBr, 25 mM Tris, 50 mM NaCl, 0.5 mM DTT, 0.5 mM EDTA, pH 7.5 in microbatch plates covered with 5 mL Als oil, Microbatch, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.988 α = 90 b = 137.334 β = 95.98 c = 148.101 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2007-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97856 APS 19-ID
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 2.51 50 95.11 124512 124512 -3 -3
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 2dhq 2.52 50 118244 6267 95.13 0.20008 0.19754 0.1977 0.24779 0.2463 RANDOM 37.126
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] 0.12 0.88 0.32 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.675 r_dihedral_angle_3_deg 13.862 r_dihedral_angle_4_deg 10.386 r_dihedral_angle_1_deg 4.559 r_angle_refined_deg 0.882 r_scangle_it 0.518 r_mcangle_it 0.366 r_scbond_it 0.299 r_nbtor_refined 0.29 r_mcbond_it 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.675 r_dihedral_angle_3_deg 13.862 r_dihedral_angle_4_deg 10.386 r_dihedral_angle_1_deg 4.559 r_angle_refined_deg 0.882 r_scangle_it 0.518 r_mcangle_it 0.366 r_scbond_it 0.299 r_nbtor_refined 0.29 r_mcbond_it 0.204 r_symmetry_vdw_refined 0.19 r_nbd_refined 0.159 r_xyhbond_nbd_refined 0.088 r_symmetry_hbond_refined 0.088 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 24621 Nucleic Acid Atoms Solvent Atoms 1604 Heterogen Atoms 48
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling