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Crystal structure of Arabidopsis thaliana HPPD complexed with iptriazopyrid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M sodium citrate (pH 5.0), 32 or 28 vol% polyethylene glycol (PEG) 400, and 15 or 10 vol% 2-propanol
2 mM iptriazopyrid and 2 mM CoCl2
Crystal Properties Matthews coefficient Solvent content 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.16 α = 90 b = 96.04 β = 92.806 c = 97.82 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 95 PIXEL DECTRIS EIGER X 4M 2023-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.025 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.15 50 99.7 0.239 0.991 6.14 6.69 96459
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.28 98.9 2.988 0.421 0.6 5.63
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 1SP9 2.15 48.022 94904 4744 98.139 0.214 0.211 0.2176 0.2662 0.2687 49.468
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] 0.022 0.001 -0.006 -0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.077 r_dihedral_angle_3_deg 15.182 r_dihedral_angle_6_deg 13.024 r_dihedral_angle_other_2_deg 12.612 r_lrange_it 8.334 r_lrange_other 8.329 r_dihedral_angle_1_deg 6.722 r_scangle_it 5.723 r_scangle_other 5.723 r_mcangle_it 4.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.077 r_dihedral_angle_3_deg 15.182 r_dihedral_angle_6_deg 13.024 r_dihedral_angle_other_2_deg 12.612 r_lrange_it 8.334 r_lrange_other 8.329 r_dihedral_angle_1_deg 6.722 r_scangle_it 5.723 r_scangle_other 5.723 r_mcangle_it 4.937 r_mcangle_other 4.936 r_scbond_it 3.681 r_scbond_other 3.681 r_mcbond_it 3.179 r_mcbond_other 3.179 r_angle_refined_deg 1.24 r_angle_other_deg 0.438 r_nbd_other 0.231 r_symmetry_nbd_other 0.204 r_nbd_refined 0.203 r_symmetry_nbd_refined 0.196 r_symmetry_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.057 r_symmetry_xyhbond_nbd_other 0.028 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12352 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing