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Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli.
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 7.1 293 20% PEG 3350
200 mM Sodium Tartrate
14.7 mM HEPES pH 7.1
Crystal Properties Matthews coefficient Solvent content 2.49 50.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.714 α = 90 b = 161.492 β = 90 c = 137.325 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 200K VeriMaxHF 2015-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.1 81 99.9 0.142 0.052 14.4 6.8 35248
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 0.462 0.236 0.968
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 1yxc 2.1 27.51 35248 1850 99.77 0.1703 0.1683 0.1786 0.2071 0.2147 RANDOM 16.603
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] 0.05 -0.22 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.472 r_dihedral_angle_4_deg 21.853 r_dihedral_angle_3_deg 14.852 r_dihedral_angle_1_deg 7.155 r_angle_refined_deg 1.695 r_angle_other_deg 1.442 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.472 r_dihedral_angle_4_deg 21.853 r_dihedral_angle_3_deg 14.852 r_dihedral_angle_1_deg 7.155 r_angle_refined_deg 1.695 r_angle_other_deg 1.442 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4421 Nucleic Acid Atoms Solvent Atoms 514 Heterogen Atoms 2037
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling PHASER phasing