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Structure of E. coli dihydrodipicolinate synthase bound with allosteric inhibitor (S)-lysine to 2.0 A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 276 1.8M potassium phosphate, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 276K
Crystal Properties Matthews coefficient Solvent content 3.72 66.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.148 α = 90 b = 121.148 β = 90 c = 110.084 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE RIGAKU RAXIS IV 2004-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 37.99 100 0.088 14.9 10.88 63306 2 2
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 2.07 100 0.356 6.1 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 37.99 60077 3225 100 0.16074 0.15933 0.1723 0.18611 0.1761 RANDOM 19.854
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] -0.18 -0.09 -0.18 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.849 r_dihedral_angle_4_deg 17.089 r_dihedral_angle_3_deg 15.372 r_dihedral_angle_1_deg 6.125 r_scangle_it 3.779 r_scbond_it 2.357 r_angle_refined_deg 1.531 r_mcangle_it 1.307 r_angle_other_deg 0.901 r_mcbond_it 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.849 r_dihedral_angle_4_deg 17.089 r_dihedral_angle_3_deg 15.372 r_dihedral_angle_1_deg 6.125 r_scangle_it 3.779 r_scbond_it 2.357 r_angle_refined_deg 1.531 r_mcangle_it 1.307 r_angle_other_deg 0.901 r_mcbond_it 0.7 r_symmetry_hbond_refined 0.272 r_symmetry_vdw_other 0.252 r_nbd_refined 0.233 r_nbd_other 0.186 r_mcbond_other 0.179 r_symmetry_vdw_refined 0.173 r_nbtor_refined 0.168 r_metal_ion_refined 0.163 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.101 r_nbtor_other 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4321 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling AMoRE phasing