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Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Providencia alcalifaciens complexed with quinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25%w/v PEG3350, 0.2M Magnesium chloride, 0.1M bis Tris PH-5.5, 20% ETG
Crystal Properties Matthews coefficient Solvent content 2.59 52.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.978 α = 90 b = 51.823 β = 108.93 c = 133.303 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU HyPix-6000HE 2022-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54184
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 2.68 25.21 96.8 0.943 4.5 3.5 43906
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 2.68 2.78 97.8 0.699 1.2
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 1KFL 2.68 25.21 41750 2152 96.68 0.2667 0.26468 0.2753 0.30539 0.3068 RANDOM 34.944
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] 0.37 0.08 -1.42 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.581 r_dihedral_angle_2_deg 12.415 r_long_range_B_refined 11.333 r_long_range_B_other 11.333 r_scangle_other 8.911 r_mcangle_it 7.766 r_mcangle_other 7.766 r_dihedral_angle_1_deg 7.107 r_scbond_it 5.882 r_scbond_other 5.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.581 r_dihedral_angle_2_deg 12.415 r_long_range_B_refined 11.333 r_long_range_B_other 11.333 r_scangle_other 8.911 r_mcangle_it 7.766 r_mcangle_other 7.766 r_dihedral_angle_1_deg 7.107 r_scbond_it 5.882 r_scbond_other 5.882 r_mcbond_it 5.166 r_mcbond_other 5.166 r_angle_refined_deg 2.549 r_angle_other_deg 0.826 r_chiral_restr 0.111 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9148 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing