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Crystal structure of Oryza sativa HPPD
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 acetate (pH 4.5), 20 vol% PEG1000, and 0.2 M zinc acetate
2 mM CoCl2
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.11 α = 101.387 b = 64.59 β = 107.961 c = 73.16 γ = 97
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 2024-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.02 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 50 97.9 0.168 0.978 6.92 3.69 65758
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 2.12 95.3 0.842 0.622 2.03 3.32
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 45.94 65758 3288 98.328 0.195 0.1936 0.2013 0.2265 0.2308 28.281
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] -0.003 -0.002 -0.002 0.002 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.724 r_dihedral_angle_6_deg 13.676 r_dihedral_angle_2_deg 10.726 r_dihedral_angle_1_deg 6.782 r_lrange_it 5.744 r_lrange_other 5.656 r_scangle_it 3.776 r_scangle_other 3.775 r_mcangle_it 3.008 r_mcangle_other 3.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.724 r_dihedral_angle_6_deg 13.676 r_dihedral_angle_2_deg 10.726 r_dihedral_angle_1_deg 6.782 r_lrange_it 5.744 r_lrange_other 5.656 r_scangle_it 3.776 r_scangle_other 3.775 r_mcangle_it 3.008 r_mcangle_other 3.008 r_scbond_it 2.279 r_scbond_other 2.279 r_mcbond_it 1.843 r_mcbond_other 1.839 r_angle_refined_deg 1.315 r_angle_other_deg 0.464 r_symmetry_xyhbond_nbd_refined 0.348 r_nbd_other 0.242 r_symmetry_nbd_refined 0.235 r_nbd_refined 0.2 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.172 r_xyhbond_nbd_other 0.138 r_metal_ion_refined 0.109 r_symmetry_metal_ion_refined 0.099 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.072 r_chiral_restr 0.062 r_gen_planes_refined 0.005 r_bond_refined_d 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 5995 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing