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Crystal structure of N-acetylornithine glutamate acetyltransferase (ZmNAOGAT) from Zea mays (maize) in complex with ornithine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VRA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 22 mg/ml protein concentration, HEPES ph 5.5, 30% PEG 3350, soaked with 10 mM AcCoA + 10 mM ORN for 10 minutes; crystal cryoprotected with 25% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.13 42.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.316 α = 90 b = 79.775 β = 90 c = 160.922 γ = 90
Symmetry Space Group P 21 21 21
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) Rrim I (All) Rpim I (All) 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 44.51 95.2 0.083 0.086 0.023 17.2 13.5 304832
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.06 68.7 0.66 0.19 12.2
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 44.51 282078 14705 72.78 0.12431 0.12361 0.123 0.13773 0.1379 RANDOM 12.424
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] -0.96 0.48 0.47
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 22.07 r_long_range_B_other 16.589 r_dihedral_angle_2_deg 11.936 r_dihedral_angle_3_deg 11.762 r_scangle_other 7.456 r_dihedral_angle_1_deg 6.508 r_scbond_it 5.214 r_scbond_other 5.214 r_mcangle_it 5.175 r_mcangle_other 5.175
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 22.07 r_long_range_B_other 16.589 r_dihedral_angle_2_deg 11.936 r_dihedral_angle_3_deg 11.762 r_scangle_other 7.456 r_dihedral_angle_1_deg 6.508 r_scbond_it 5.214 r_scbond_other 5.214 r_mcangle_it 5.175 r_mcangle_other 5.175 r_rigid_bond_restr 3.757 r_mcbond_it 3.486 r_mcbond_other 3.483 r_angle_refined_deg 1.3 r_angle_other_deg 0.691 r_chiral_restr 0.09 r_bond_other_d 0.029 r_bond_refined_d 0.02 r_gen_planes_refined 0.018 r_gen_planes_other 0.016 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 6104 Nucleic Acid Atoms Solvent Atoms 1141 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing