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Crystal structure of a Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (Apo, Orthorhombic P form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 35YG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 200 mM NaF, 25% PEG 3350, BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. plate 20994 B6 drop 3, Puck: PSL-2513, Cryo: 20% ethylene glycol + 80% crystallant
Crystal Properties Matthews coefficient Solvent content 2.34 47.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.621 α = 90 b = 103.556 β = 90 c = 151.285 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 EIGER2 XE 9M 2026-06-13 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 2.05 48.99 100 0.123 0.128 0.035 0.999 13.8 13.5 100704
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 2.05 2.09 100 1.635 1.699 0.458 0.752 1.7
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 2.05 48.99 1.33 100613 5133 99.99 0.1855 0.1833 0.1872 0.2284 0.231
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 15.088 f_angle_d 0.626 f_chiral_restr 0.047 f_plane_restr 0.007 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11539 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction