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Crystal structure of acetylated intermediate of N-acetylornithine glutamate acetyltransferase (ZmNAOGAT) from Zea mays (maize)
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 5 295 22mg/ml protein concentration, citrate-phosphate buffer ph 5.0, 25% PEG Smear Broad, cocrystallized with 10 mM of acetylglutamate; crystal cryoprotected with 25% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.598 α = 90 b = 80.948 β = 90 c = 161.202 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 PILATUS3 X 6M 2025-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.22 48.04 96.1 0.092 0.026 0.999 19.1 13.1 199020
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.22 1.286 0.747 0.223 0.826 3.7
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 1.22 48.04 189000 10020 85.98 0.12211 0.12092 0.161 0.14454 0.1757 RANDOM 10.637
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] -1.55 1.49 0.06
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.649 r_long_range_B_other 13.165 r_dihedral_angle_3_deg 11.112 r_dihedral_angle_2_deg 9.228 r_scangle_other 6.992 r_dihedral_angle_1_deg 5.729 r_scbond_it 4.819 r_mcangle_other 4.764 r_mcangle_it 4.76 r_scbond_other 4.758
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.649 r_long_range_B_other 13.165 r_dihedral_angle_3_deg 11.112 r_dihedral_angle_2_deg 9.228 r_scangle_other 6.992 r_dihedral_angle_1_deg 5.729 r_scbond_it 4.819 r_mcangle_other 4.764 r_mcangle_it 4.76 r_scbond_other 4.758 r_rigid_bond_restr 3.754 r_mcbond_it 3.174 r_mcbond_other 3.165 r_angle_refined_deg 1.917 r_angle_other_deg 0.71 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6074 Nucleic Acid Atoms Solvent Atoms 1230 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing