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ATP phosphoribosyltransferase (HisZG ATPPRT) from Acinetobacter baumanii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M8H chains A and E used for molecular replacement
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2M sodium nitrate, 0.1M bis-Tris propane pH 8.5, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.271 α = 90 b = 172.821 β = 90.97 c = 98.109 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU SATURN 944+ mirrors 2021-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 2.4 30.82 95.6 0.124 0.135 0.051 0.996 9.6 6.4 99446
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 2.4 2.44 80.6 1.045 1.164 0.498 0.618 4.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 30.82 94223 5033 95.3 0.23959 0.23826 0.2418 0.26424 0.2694 RANDOM 49.623
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] 3.25 -0.38 0.75 -3.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.753 r_dihedral_angle_1_deg 6.482 r_dihedral_angle_2_deg 5.366 r_long_range_B_refined 3.551 r_long_range_B_other 3.551 r_scangle_other 1.764 r_mcangle_it 1.72 r_mcangle_other 1.72 r_scbond_it 1.025 r_scbond_other 1.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.753 r_dihedral_angle_1_deg 6.482 r_dihedral_angle_2_deg 5.366 r_long_range_B_refined 3.551 r_long_range_B_other 3.551 r_scangle_other 1.764 r_mcangle_it 1.72 r_mcangle_other 1.72 r_scbond_it 1.025 r_scbond_other 1.025 r_mcbond_it 0.996 r_mcbond_other 0.996 r_angle_refined_deg 0.931 r_angle_other_deg 0.324 r_chiral_restr 0.045 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17980 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling iMOSFLM data reduction PHASER phasing