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Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with Adenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DY0 2DY0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 100 mM Tris-HCl pH 8.0, 20 % PEG 4000, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.18 43.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.656 α = 90 b = 87.073 β = 111.2 c = 47.83 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 PIXEL DECTRIS EIGER2 X 16M Toroidal mirror 2022-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 1.498 41.63 99.8 0.07 0.078 0.034 0.99 12.1 5.2 54573
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 1.498 1.524 100 0.727 0.805 0.342 0.812 2.2 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2DY0 1.5 41.63 51805 2723 99.67 0.17205 0.17093 0.1802 0.19326 0.2046 RANDOM 20.831
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] -0.72 -0.88 0.9 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.847 r_dihedral_angle_4_deg 23.15 r_dihedral_angle_3_deg 12.579 r_dihedral_angle_1_deg 6.777 r_long_range_B_refined 5.719 r_long_range_B_other 5.71 r_scangle_other 4.523 r_scbond_it 3.018 r_scbond_other 3.017 r_mcangle_it 2.641
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.847 r_dihedral_angle_4_deg 23.15 r_dihedral_angle_3_deg 12.579 r_dihedral_angle_1_deg 6.777 r_long_range_B_refined 5.719 r_long_range_B_other 5.71 r_scangle_other 4.523 r_scbond_it 3.018 r_scbond_other 3.017 r_mcangle_it 2.641 r_mcangle_other 2.64 r_mcbond_it 1.853 r_mcbond_other 1.852 r_angle_refined_deg 1.756 r_angle_other_deg 1.496 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2788 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing