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Crystal structure of short-form ATP-phosphoribosyltransferase from Acinetobacter baumannii at 2.43 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 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.975 α = 90 b = 75.017 β = 90 c = 96.726 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 2.43 40.681 99.1 0.111 0.129 0.066 0.996 11.3 7.1 20950 45.9
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 2.43 2.52 98.7 0.688 0.798 0.402 0.892 2.5 7.4
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 2.43 40.681 20872 1501 98.597 0.249 0.2469 0.2503 0.2808 0.2874 49.996
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] 2.867 1.672 -4.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.046 r_dihedral_angle_6_deg 13.817 r_dihedral_angle_2_deg 10.891 r_lrange_it 10.282 r_lrange_other 10.277 r_dihedral_angle_1_deg 7.341 r_scangle_it 7.274 r_scangle_other 7.273 r_mcangle_other 6.199 r_mcangle_it 6.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.046 r_dihedral_angle_6_deg 13.817 r_dihedral_angle_2_deg 10.891 r_lrange_it 10.282 r_lrange_other 10.277 r_dihedral_angle_1_deg 7.341 r_scangle_it 7.274 r_scangle_other 7.273 r_mcangle_other 6.199 r_mcangle_it 6.198 r_scbond_it 4.473 r_scbond_other 4.471 r_mcbond_it 3.908 r_mcbond_other 3.908 r_angle_refined_deg 1.448 r_angle_other_deg 0.481 r_nbd_other 0.268 r_nbd_refined 0.22 r_symmetry_nbd_other 0.208 r_symmetry_xyhbond_nbd_other 0.203 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.17 r_metal_ion_refined 0.138 r_symmetry_nbd_refined 0.116 r_symmetry_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 186 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building