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Crystal structure of ornithine transcarbamylase from Arabidopsis thaliana (AtOTC) in complex with ornithine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG 3350 16%, Lithium sulfate 0.3M, HEPES 0.1M pH 6.0, 20mM ornithine, cryoprotection was obtained by 25% PEG400
Crystal Properties Matthews coefficient Solvent content 3.21 61.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.307 α = 90 b = 155.38 β = 90 c = 189.541 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 6M 2023-02-22 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) 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 1.5 50 99.6 0.072 0.999 17.88 7.33 208445
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 1.5 1.59 98.9 0.933 0.731 2.05 7.14
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 1.5 49.02 207402 1043 99.55 0.11945 0.11927 0.1675 0.15603 0.1897 RANDOM 19.788
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] 0.72 -0.21 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.2 r_dihedral_angle_2_deg 10.556 r_dihedral_angle_1_deg 6.19 r_long_range_B_refined 4.388 r_rigid_bond_restr 4.273 r_long_range_B_other 3.627 r_scangle_other 2.516 r_mcangle_it 2.174 r_mcangle_other 2.174 r_scbond_other 1.942
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.2 r_dihedral_angle_2_deg 10.556 r_dihedral_angle_1_deg 6.19 r_long_range_B_refined 4.388 r_rigid_bond_restr 4.273 r_long_range_B_other 3.627 r_scangle_other 2.516 r_mcangle_it 2.174 r_mcangle_other 2.174 r_scbond_other 1.942 r_scbond_it 1.941 r_angle_refined_deg 1.702 r_mcbond_it 1.548 r_mcbond_other 1.548 r_angle_other_deg 0.622 r_chiral_restr 0.097 r_bond_refined_d 0.012 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 7189 Nucleic Acid Atoms Solvent Atoms 1278 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing PHENIX model building