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Crystal structure of acetylated intermediate of N-acetylornithine glutamate acetyltransferase (OsNAOGAT) from Oryza sativa (rice) in complex with ornithine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VRA Solution was done using unpublished structure of Arabidopsis thaliana NAOGAT, solved using 1VRA model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 300 15 mg/ml protein concentration, 0.1M Bis-Tris pH 6.5, 0.15M MgCl2, 30% PEG 3350, 10 mM glutamate, 10 mM CoA, acetylornithine soak for 40 minutes; crystal cryoprotected with 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.18 43.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.7 α = 90 b = 55.68 β = 94.3 c = 81.3 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 PIXEL DECTRIS EIGER X 16M 2024-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.729 MAX IV BioMAX
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 1.45 44.76 97 0.04 0.999 20.32 4.4 129373
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 1.45 1.54 0.332 0.893
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.45 44.76 127272 2100 97.05 0.11257 0.11217 0.1202 0.13601 0.1454 RANDOM 19.385
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] -2.47 2.59 -1.1 3.14
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 17.657 r_long_range_B_other 14.875 r_dihedral_angle_2_deg 12.06 r_dihedral_angle_3_deg 11.423 r_scangle_other 10.511 r_scbond_it 7.411 r_scbond_other 7.411 r_mcangle_other 7.115 r_mcangle_it 7.114 r_dihedral_angle_1_deg 5.861
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 17.657 r_long_range_B_other 14.875 r_dihedral_angle_2_deg 12.06 r_dihedral_angle_3_deg 11.423 r_scangle_other 10.511 r_scbond_it 7.411 r_scbond_other 7.411 r_mcangle_other 7.115 r_mcangle_it 7.114 r_dihedral_angle_1_deg 5.861 r_mcbond_it 5.104 r_mcbond_other 5.095 r_rigid_bond_restr 3.888 r_angle_refined_deg 1.723 r_angle_other_deg 0.606 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6132 Nucleic Acid Atoms Solvent Atoms 881 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing