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E. coli dihydrodipicolinate synthase with first substrate, pyruvate, bound in active site
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 10 277 1.8M K2HPO4, N-octyl-beta-(R)-glucopyranoside, pH 10, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.7 66.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.95 α = 90 b = 120.95 β = 90 c = 110.03 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 OSMIC BLUE MIRRORS 2005-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 32.14 99.6 0.083 10.4 4.08 62822 3 25.2
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 32.14 62813 3143 99.61 0.191 0.188 0.1901 0.245 0.2443 RANDOM 27.838
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.514 r_dihedral_angle_4_deg 17.64 r_dihedral_angle_3_deg 16.054 r_dihedral_angle_1_deg 7.562 r_scangle_it 4.769 r_scbond_it 3.37 r_mcangle_it 1.888 r_angle_refined_deg 1.221 r_mcbond_it 1.156 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.514 r_dihedral_angle_4_deg 17.64 r_dihedral_angle_3_deg 16.054 r_dihedral_angle_1_deg 7.562 r_scangle_it 4.769 r_scbond_it 3.37 r_mcangle_it 1.888 r_angle_refined_deg 1.221 r_mcbond_it 1.156 r_nbtor_refined 0.305 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.214 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.163 r_metal_ion_refined 0.103 r_chiral_restr 0.096 r_gen_planes_refined 0.012 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4390 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 26
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction