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Crystal structure of ornithine transcarbamylase from Arabidopsis thaliana (AtOTC) in complex with carbamoyl phosphate
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 293 PEG 3350 26%, Lithium sulfate 0.3M, HEPES 0.1M pH 6.0, 20mM carbamoyl phosphate, cryoprotection was obtained by 25% PEG400
Crystal Properties Matthews coefficient Solvent content 3.29 62.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.247 α = 90 b = 154.601 β = 90 c = 191.768 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 1.55 50 99.2 0.172 0.982 5.25 5.51 194853
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 1.55 1.64 97.5 0.957 0.563 1.16
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 1.55 44.67 187213 1872 98.97 0.18473 0.1844 0.1961 0.21942 0.2259 RANDOM 20.606
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] 0.08 0.2 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.862 r_dihedral_angle_2_deg 10.192 r_long_range_B_refined 8.258 r_long_range_B_other 8.258 r_dihedral_angle_1_deg 6.452 r_scangle_other 2.071 r_angle_refined_deg 1.774 r_scbond_it 1.483 r_scbond_other 1.483 r_mcangle_other 1.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.862 r_dihedral_angle_2_deg 10.192 r_long_range_B_refined 8.258 r_long_range_B_other 8.258 r_dihedral_angle_1_deg 6.452 r_scangle_other 2.071 r_angle_refined_deg 1.774 r_scbond_it 1.483 r_scbond_other 1.483 r_mcangle_other 1.109 r_mcangle_it 1.108 r_mcbond_it 0.683 r_mcbond_other 0.683 r_angle_other_deg 0.601 r_chiral_restr 0.099 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7073 Nucleic Acid Atoms Solvent Atoms 1190 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing PHENIX model building