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Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (ATP complex)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q13UJ9-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 BRK E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ATP, plate 20558 E6 drop 1, Puck: PSL-1913, Cryo: 20% PEG 200 + 80% crystallant
Crystal Properties Matthews coefficient Solvent content 2.86 57.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.007 α = 90 b = 170.436 β = 90 c = 170.508 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 2025-11-10 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 1.93 47.28 99.5 0.146 0.151 0.041 0.998 15 13.7 146557
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 1.93 1.98 98.8 1.957 2.028 0.53 0.759 14.4
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 1.93 44.81 1.34 146422 7285 99.44 0.1704 0.1691 0.1741 0.1956 0.1991
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 13.008 f_angle_d 1.033 f_chiral_restr 0.06 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11473 Nucleic Acid Atoms Solvent Atoms 730 Heterogen Atoms 185
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction