☰ Navigation Tabs
Crystal structure of dihydrodipicolinate synthase from Pseudomonas aeruginosa(PsDHDPS)complexed with L-lysine at 2.65A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% PEG 3350, 70mM Tris-HCl, 170mM MgCl2, 6% Propylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.34 α = 90 b = 81.84 β = 90 c = 81.78 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH Mirror 2010-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.65 57.8 97.9 0.115 10 16422 16422
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.68 99 0.335 3.5
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 (All) 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 3NOE 2.65 33.27 15446 15446 826 99.09 0.2178 0.21773 0.21563 0.25546 0.2439 RANDOM 21.364
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 -0.54 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.829 r_dihedral_angle_4_deg 18.15 r_dihedral_angle_3_deg 17.494 r_scangle_it 3.344 r_dihedral_angle_1_deg 2.975 r_scbond_it 2.13 r_mcangle_it 1.828 r_angle_refined_deg 1.45 r_mcbond_it 1.022 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.829 r_dihedral_angle_4_deg 18.15 r_dihedral_angle_3_deg 17.494 r_scangle_it 3.344 r_dihedral_angle_1_deg 2.975 r_scbond_it 2.13 r_mcangle_it 1.828 r_angle_refined_deg 1.45 r_mcbond_it 1.022 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 4400 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling