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Crystal structure of the short-form ATP-phosphoribosyltransferase from Acinetobacter baumannii at 2.3 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 23FI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 Sodium acetate trihydrate, Sodium formate
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.844 α = 90 b = 75.213 β = 90 c = 96.98 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 CCD MARMOSAIC 225 mm CCD 2026-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.980 RRCAT INDUS-2 PX-BL21
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 2.3 40.75 100 0.081 0.088 0.033 0.998 22.7 13.7 25015 41.8
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 2.3 2.38 100 0.561 0.602 0.216 0.968 4.4 14.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 37.635 24813 753 99.339 0.234 0.2326 0.236 0.2729 0.2741 47.609
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] 3.159 0.787 -3.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.861 r_dihedral_angle_6_deg 14.754 r_dihedral_angle_3_deg 14.392 r_lrange_other 11.863 r_lrange_it 11.841 r_scangle_it 8.017 r_scangle_other 8.016 r_dihedral_angle_1_deg 7.089 r_mcangle_it 6.493 r_mcangle_other 6.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.861 r_dihedral_angle_6_deg 14.754 r_dihedral_angle_3_deg 14.392 r_lrange_other 11.863 r_lrange_it 11.841 r_scangle_it 8.017 r_scangle_other 8.016 r_dihedral_angle_1_deg 7.089 r_mcangle_it 6.493 r_mcangle_other 6.491 r_scbond_it 5.152 r_scbond_other 5.121 r_mcbond_it 4.353 r_mcbond_other 4.352 r_angle_refined_deg 1.783 r_angle_other_deg 0.559 r_nbd_other 0.321 r_nbd_refined 0.226 r_symmetry_nbd_other 0.212 r_symmetry_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.187 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.174 r_metal_ion_refined 0.116 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3470 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building