☰ Navigation Tabs
Type II dehydroquinase from Mycobacterium tuberculosis complexed with citrazinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N59 PDB entry 3N59
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, 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 Al s oil, Microbatch, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.15 42.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.316 α = 90 b = 137.208 β = 96.59 c = 146.713 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 MARMOSAIC 300 mm CCD 2008-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97934 APS 23-ID-B
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 1.77 50 98.44 176635 176635 -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 3N59 2.25 50 167784 8851 98.43 0.20636 0.20479 0.2046 0.23612 0.2351 RANDOM 43.441
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] -0.25 0.21 0.33 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.252 r_dihedral_angle_3_deg 14.404 r_dihedral_angle_4_deg 13.442 r_dihedral_angle_1_deg 4.435 r_angle_refined_deg 0.881 r_scangle_it 0.643 r_scbond_it 0.362 r_nbtor_refined 0.29 r_mcangle_it 0.229 r_nbd_refined 0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.252 r_dihedral_angle_3_deg 14.404 r_dihedral_angle_4_deg 13.442 r_dihedral_angle_1_deg 4.435 r_angle_refined_deg 0.881 r_scangle_it 0.643 r_scbond_it 0.362 r_nbtor_refined 0.29 r_mcangle_it 0.229 r_nbd_refined 0.159 r_symmetry_vdw_refined 0.15 r_mcbond_it 0.117 r_xyhbond_nbd_refined 0.088 r_symmetry_hbond_refined 0.077 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 25582 Nucleic Acid Atoms Solvent Atoms 1307 Heterogen Atoms 268
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling