☰ Navigation Tabs
Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 292 100 mM Tris-HCl, 28 % PEG 4000, 170 mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.08 40.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.79 α = 90 b = 87.37 β = 107.78 c = 139.85 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 MARRESEARCH 2004-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 2.28 99 99.7 0.085 27.98 99893 -3
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 2.28 2.32 95 0.192 12.53
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1O5K 2.28 30 99362 97308 1987 100 0.149 0.148 0.215 0.2596 RANDOM 29.5
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] -0.71 -1.07 1.44 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.971 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 13.805 r_dihedral_angle_1_deg 6.496 r_scangle_it 5.89 r_scbond_it 4.049 r_angle_refined_deg 1.628 r_mcangle_it 1.53 r_mcbond_it 0.943 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.971 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 13.805 r_dihedral_angle_1_deg 6.496 r_scangle_it 5.89 r_scbond_it 4.049 r_angle_refined_deg 1.628 r_mcangle_it 1.53 r_mcbond_it 0.943 r_nbtor_refined 0.31 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.216 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.096 r_bond_refined_d 0.018 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17072 Nucleic Acid Atoms Solvent Atoms 1587 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing