☰ Navigation Tabs
Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Index F12: 100 mM HEPES, pH 7.5, 25% PEG 3350, 200 mM NaCl. BuxeA.00088.a.B2.PW39423 at 24.5 mg/mL. plate 20257 F12 drop 1, Puck: PSL-0410, Cryo: 20% glycerol + 80% crystallant
Crystal Properties Matthews coefficient Solvent content 3.25 62.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.57 α = 90 b = 157.57 β = 90 c = 138.457 γ = 120
Symmetry Space Group P 3 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 EIGER2 XE 9M 2025-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.55 48.6 100 0.111 0.114 0.025 1 24.4 20.3 64960
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.62 100 2.204 2.258 0.49 0.667 21.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.55 48.6 1.34 64945 3313 99.98 0.192 0.1902 0.1941 0.2265 0.2293
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.916 f_angle_d 0.527 f_chiral_restr 0.041 f_plane_restr 0.006 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10243 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction