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Dihydrodipicolinate synthase co-crystallised with (S)-lysine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 284 20mM Tris HCl, 10mM (S)-lysine, pH 8, 1.8M K2HPO4, pH 10, N-octyl-R-glucopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties Matthews coefficient Solvent content 3.75 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.68 α = 90 b = 121.68 β = 90 c = 109.799 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 110 IMAGE PLATE RIGAKU RAXIS IV 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 1.9 33.5 99.4 0.091 3.82 73712 3 3 20.5
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) 1.9 1.97 100 0.342 3.5 3.71
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 (All) 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 1.9 25.8 70002 3688 100 0.16924 0.16924 0.16758 0.1775 0.20154 0.2091 RANDOM 17.71
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] -0.43 -0.22 -0.43 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.974 r_dihedral_angle_4_deg 18.834 r_dihedral_angle_3_deg 13.292 r_dihedral_angle_1_deg 6.007 r_scangle_it 3.603 r_scbond_it 2.23 r_angle_refined_deg 1.395 r_mcangle_it 1.166 r_angle_other_deg 0.853 r_mcbond_it 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.974 r_dihedral_angle_4_deg 18.834 r_dihedral_angle_3_deg 13.292 r_dihedral_angle_1_deg 6.007 r_scangle_it 3.603 r_scbond_it 2.23 r_angle_refined_deg 1.395 r_mcangle_it 1.166 r_angle_other_deg 0.853 r_mcbond_it 0.63 r_symmetry_hbond_refined 0.348 r_symmetry_vdw_other 0.263 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.195 r_nbd_other 0.186 r_mcbond_other 0.169 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.146 r_metal_ion_refined 0.095 r_nbtor_other 0.09 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4313 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement AMoRE phasing