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Crystal structure of short-form adenosine triphosphate phosphoribosyltransferase from Acinetobacter baumannii at 1.94 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JUK
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 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.717 α = 90 b = 75.234 β = 90 c = 96.885 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 X 9M 2023-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
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 1.94 46.51 99.6 0.112 0.121 0.046 0.999 12.8 13.4 40845 42.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.01 2.95 1.138 0.55 0.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.942 46.51 40708 1956 99.314 0.189 0.1862 0.2368 0.2378 52.088
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] 1.342 2.377 -3.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.318 r_dihedral_angle_6_deg 12.964 r_lrange_other 10.82 r_lrange_it 10.803 r_scangle_it 7.976 r_scangle_other 7.974 r_dihedral_angle_1_deg 6.896 r_dihedral_angle_2_deg 6.024 r_mcangle_it 5.829 r_mcangle_other 5.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.318 r_dihedral_angle_6_deg 12.964 r_lrange_other 10.82 r_lrange_it 10.803 r_scangle_it 7.976 r_scangle_other 7.974 r_dihedral_angle_1_deg 6.896 r_dihedral_angle_2_deg 6.024 r_mcangle_it 5.829 r_mcangle_other 5.828 r_scbond_it 5.228 r_scbond_other 5.226 r_mcbond_it 4.205 r_mcbond_other 4.201 r_angle_refined_deg 1.471 r_angle_other_deg 0.486 r_nbd_refined 0.211 r_symmetry_nbd_other 0.202 r_nbd_other 0.2 r_symmetry_xyhbond_nbd_refined 0.192 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.171 r_ncsr_local_group_1 0.112 r_symmetry_nbd_refined 0.087 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.072 r_bond_refined_d 0.006 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 3486 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building MxCuBE data collection