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Structure of E. coli dihydrodipicolinate synthase to 1.9 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DHP
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 3.71 66.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.869 α = 90 b = 120.869 β = 90 c = 110.194 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 2004-08-31 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 39.57 99.7 0.089 9.7 4.3 73225 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) 1.9 1.97 99.9 0.358 3.5 4.17
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1dhp 1.9 39.56 69522 3700 100 0.17371 0.17175 0.1805 0.21145 0.2189 RANDOM 19.915
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] -0.11 -0.06 -0.11 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.585 r_dihedral_angle_4_deg 18.511 r_dihedral_angle_3_deg 15.108 r_dihedral_angle_1_deg 6.439 r_scangle_it 3.885 r_scbond_it 2.381 r_angle_refined_deg 1.57 r_mcangle_it 1.343 r_angle_other_deg 0.901 r_mcbond_it 0.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.585 r_dihedral_angle_4_deg 18.511 r_dihedral_angle_3_deg 15.108 r_dihedral_angle_1_deg 6.439 r_scangle_it 3.885 r_scbond_it 2.381 r_angle_refined_deg 1.57 r_mcangle_it 1.343 r_angle_other_deg 0.901 r_mcbond_it 0.754 r_symmetry_vdw_other 0.233 r_nbd_refined 0.232 r_mcbond_other 0.209 r_symmetry_vdw_refined 0.199 r_nbd_other 0.187 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.159 r_metal_ion_refined 0.124 r_chiral_restr 0.102 r_nbtor_other 0.094 r_bond_refined_d 0.015 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 4304 Nucleic Acid Atoms Solvent Atoms 616 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling AMoRE phasing