☰ Navigation Tabs
The three dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HKV PDB ENTRY 1HKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 291 20-23%(w/v) polyethylene glycol monomethylether 5000, 0.1 M MES, 60 mM ammonium sulfate, pH 6.1-6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.78 α = 90 b = 106.88 β = 104.99 c = 121.93 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 MAR CCD 165 mm 2004-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.33 99 99.9 0.077 17.8 4 80203 42.5
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 2.33 2.37 99.9 0.623 2.3
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 1HKV 2.33 30 78557 1597 99.9 0.192 0.191 0.194 0.241 0.2407 RANDOM 46.01
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] 1.54 -1.52 -1.69 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.421 r_dihedral_angle_4_deg 20.851 r_dihedral_angle_3_deg 18.379 r_dihedral_angle_1_deg 6.481 r_scangle_it 5.851 r_scbond_it 4.166 r_angle_refined_deg 1.788 r_mcangle_it 1.643 r_mcbond_it 0.924 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.421 r_dihedral_angle_4_deg 20.851 r_dihedral_angle_3_deg 18.379 r_dihedral_angle_1_deg 6.481 r_scangle_it 5.851 r_scbond_it 4.166 r_angle_refined_deg 1.788 r_mcangle_it 1.643 r_mcbond_it 0.924 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.289 r_symmetry_hbond_refined 0.242 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 13350 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing