☰ Navigation Tabs
Dihydrodipicolinate synthase mutant - K161A - with the substrate pyruvate bound in the active site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YXC
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 3.72 66.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.881 α = 90 b = 120.881 β = 90 c = 110.5 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 2007-10-10 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) R Sym 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 2.3 32.17 95 0.088 0.088 7.4 3.42 39830 39830 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 97.3 0.35 0.35 2.8 3.27
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1yxc 2.3 32.17 37802 37802 2019 94.97 0.19784 0.19582 0.1954 0.23582 0.2335 RANDOM 27.751
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] -0.12 -0.06 -0.12 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.693 r_dihedral_angle_4_deg 17.417 r_dihedral_angle_3_deg 15.394 r_dihedral_angle_1_deg 6.131 r_scangle_it 3.312 r_scbond_it 2.013 r_angle_refined_deg 1.364 r_mcangle_it 1.086 r_mcbond_it 0.561 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.693 r_dihedral_angle_4_deg 17.417 r_dihedral_angle_3_deg 15.394 r_dihedral_angle_1_deg 6.131 r_scangle_it 3.312 r_scbond_it 2.013 r_angle_refined_deg 1.364 r_mcangle_it 1.086 r_mcbond_it 0.561 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 170 Heterogen Atoms 81
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling