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The crystal structure of a dimeric mutant of Dihydrodipicolinate synthase from E.coli- DHDPS-L197Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 PEG 1500, TRIS HCL, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.09 60.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.482 α = 90 b = 106.705 β = 90 c = 120.657 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 110 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.7 39.97 99.5 0.072 10.8 3.63 86208 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 1.7 1.76 99.8 0.337 3.5
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 1.7 34.12 83961 2180 100 0.186 0.185 0.1937 0.228 0.232 RANDOM 17.16
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] -0.48 0.37 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_4_deg 20.262 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 5.97 r_scangle_it 3.28 r_scbond_it 2.239 r_angle_refined_deg 1.343 r_mcangle_it 1.17 r_mcbond_it 0.887 r_angle_other_deg 0.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_4_deg 20.262 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 5.97 r_scangle_it 3.28 r_scbond_it 2.239 r_angle_refined_deg 1.343 r_mcangle_it 1.17 r_mcbond_it 0.887 r_angle_other_deg 0.841 r_symmetry_vdw_other 0.256 r_nbd_refined 0.215 r_nbd_other 0.182 r_mcbond_other 0.181 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_other 0.109 r_nbtor_other 0.087 r_chiral_restr 0.08 r_symmetry_vdw_refined 0.062 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_metal_ion_refined 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 4394 Nucleic Acid Atoms Solvent Atoms 793 Heterogen Atoms 12
Software Software Software Name Purpose AMoRE phasing REFMAC refinement d*TREK data scaling