☰ Navigation Tabs
Structure of E. coli dihydrodipicolinate synthase complexed with hydroxypyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YXC PDB ENTRY 1YXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 285 1.8M K2HPO4 (pH 10.0), 6% w/v N-octyl-D-glucopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 3.73 67.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.967 α = 90 b = 120.967 β = 90 c = 110.639 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++ 2006-08-01 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 2.4 34.79 98.5 0.114 7.8 3.96 36400 36400
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 2.4 2.49 98.9 0.393 2.8
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 PDB ENTRY 1YXC 2.4 31.49 34563 1818 100 0.1734 0.1702 0.1785 0.23729 0.2434 RANDOM 32.2
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] -0.35 -0.17 -0.35 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.619 r_dihedral_angle_4_deg 18.22 r_dihedral_angle_3_deg 16.412 r_dihedral_angle_1_deg 7.041 r_scangle_it 4.12 r_scbond_it 2.674 r_angle_refined_deg 1.765 r_mcangle_it 1.471 r_angle_other_deg 1.095 r_mcbond_it 0.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.619 r_dihedral_angle_4_deg 18.22 r_dihedral_angle_3_deg 16.412 r_dihedral_angle_1_deg 7.041 r_scangle_it 4.12 r_scbond_it 2.674 r_angle_refined_deg 1.765 r_mcangle_it 1.471 r_angle_other_deg 1.095 r_mcbond_it 0.789 r_symmetry_vdw_other 0.293 r_symmetry_hbond_refined 0.231 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.222 r_nbd_other 0.205 r_mcbond_other 0.182 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.165 r_metal_ion_refined 0.148 r_chiral_restr 0.099 r_nbtor_other 0.093 r_bond_refined_d 0.021 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 4360 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling AMoRE phasing