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Crystal structure of short-form adenosine triphosphate phosphoribosyltransferase from Acinetobacter baumannii at 2.18 angstrom resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WGM
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 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.476 α = 90 b = 79.203 β = 90 c = 97.777 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 2023-03-01 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 2.18 97.78 99.6 0.062 0.073 0.038 0.999 13.1 6.7 29519 54.9
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 2.18 2.25 1.497 1.763 0.924 0.744 1.2
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 2.181 57.769 29464 739 99.561 0.18 0.1791 0.1906 0.2116 0.2183 65.915
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] 1.58 3.2 -4.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.63 r_dihedral_angle_6_deg 14.098 r_dihedral_angle_2_deg 13.035 r_lrange_it 13.004 r_lrange_other 12.983 r_scangle_it 9.826 r_scangle_other 9.824 r_mcangle_it 7.496 r_mcangle_other 7.495 r_dihedral_angle_1_deg 7.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.63 r_dihedral_angle_6_deg 14.098 r_dihedral_angle_2_deg 13.035 r_lrange_it 13.004 r_lrange_other 12.983 r_scangle_it 9.826 r_scangle_other 9.824 r_mcangle_it 7.496 r_mcangle_other 7.495 r_dihedral_angle_1_deg 7.394 r_scbond_it 6.491 r_scbond_other 6.491 r_mcbond_it 5.227 r_mcbond_other 5.226 r_angle_refined_deg 1.551 r_angle_other_deg 0.498 r_nbd_other 0.234 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_other 0.164 r_symmetry_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.068 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 3502 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing MxCuBE data collection Coot model building