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Crystal structure of Oryza sativa 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), 12 weight% PEG6000, and 50 mM sodium iodide
2 mM iptriazopyrid and 2 mM CoCl2
Crystal Properties Matthews coefficient Solvent content 2.82 56.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.61 α = 90 b = 158.61 β = 90 c = 84.075 γ = 90
Symmetry Space Group P 42 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 95 PIXEL DECTRIS EIGER X 4M 2024-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.018 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 2.9 50 99.8 0.26 0.997 12.39 13.4 24533
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 2.9 3.06 99.3 3.084 0.379 0.89 13.9
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 2.9 46.652 24333 1217 99.947 0.207 0.2033 0.2114 0.2855 0.2833 78.673
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] 0.001 0.001 -0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 19.189 r_dihedral_angle_3_deg 17.548 r_dihedral_angle_2_deg 16.275 r_lrange_other 13.962 r_lrange_it 13.961 r_dihedral_angle_6_deg 12.85 r_scangle_it 9.814 r_scangle_other 9.813 r_mcangle_it 9.309 r_mcangle_other 9.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 19.189 r_dihedral_angle_3_deg 17.548 r_dihedral_angle_2_deg 16.275 r_lrange_other 13.962 r_lrange_it 13.961 r_dihedral_angle_6_deg 12.85 r_scangle_it 9.814 r_scangle_other 9.813 r_mcangle_it 9.309 r_mcangle_other 9.308 r_dihedral_angle_1_deg 7.069 r_scbond_it 6.108 r_scbond_other 6.107 r_mcbond_it 5.837 r_mcbond_other 5.833 r_angle_refined_deg 1.457 r_angle_other_deg 0.522 r_metal_ion_refined 0.284 r_nbd_refined 0.222 r_nbd_other 0.215 r_symmetry_nbd_other 0.211 r_symmetry_nbd_refined 0.186 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.153 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5847 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing