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Complex structure of AtHPPD with inhibitor YH201034
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8WQM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Tris-HCl pH 8.5, 0.1M Bicine pH 8.5, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI, 25%(w/v) MPD, 25%(w/v) PEG 1000, 25%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.03 39.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.832 α = 90 b = 84.271 β = 100.28 c = 62.302 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2024-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.9791 SSRF BL10U2
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 1.8 37.799 98.61 0.998 16.17 5.9 36095
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 1.8 1.864 98.61 0.835
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 37.799 1.34 35708 1982 98.62 0.1806 0.1783 0.1809 0.2201 0.2199
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.744 f_angle_d 1.422 f_chiral_restr 0.097 f_bond_d 0.017 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2888 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing