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Crystal structure of dihydrodipicolinate synthase from Klebsiella pneumoniae bound to pyruvate
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 293 0.1 M Tris, ph 7.5, 2 M Ammonium Sulfate, 5 mM Pyruvate
Crystal Properties Matthews coefficient Solvent content 2.4 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.634 α = 90 b = 114.23 β = 90 c = 55.298 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER X 16M 2018-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.89 49.039 99.7 0.998 11.4 6.7 54112
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.93 95.3 0.827
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1YXC 1.892 48.99 54037 2562 99.666 0.171 0.1693 0.1803 0.1982 0.2071 22.372
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] -0.034 -0.847 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.125 r_dihedral_angle_4_deg 15.829 r_dihedral_angle_3_deg 13.191 r_dihedral_angle_1_deg 6.666 r_lrange_it 4.525 r_lrange_other 4.393 r_scangle_it 3.522 r_scangle_other 3.488 r_scbond_it 2.203 r_scbond_other 2.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.125 r_dihedral_angle_4_deg 15.829 r_dihedral_angle_3_deg 13.191 r_dihedral_angle_1_deg 6.666 r_lrange_it 4.525 r_lrange_other 4.393 r_scangle_it 3.522 r_scangle_other 3.488 r_scbond_it 2.203 r_scbond_other 2.179 r_mcangle_other 1.947 r_mcangle_it 1.944 r_angle_refined_deg 1.398 r_angle_other_deg 1.359 r_mcbond_it 1.32 r_mcbond_other 1.308 r_nbd_refined 0.205 r_symmetry_nbd_refined 0.185 r_symmetry_nbd_other 0.168 r_nbd_other 0.152 r_nbtor_refined 0.149 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.098 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4370 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing