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Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 2.16 43.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.014 α = 106.72 b = 47.752 β = 103.09 c = 54.074 γ = 111.02
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2021-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 48.14 92.3 0.02 0.013 1 24.5 3.9 36928
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 87.2 0.114 0.066 0.99 7.6 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 1.65 35.61 35083 1832 92.23 0.15834 0.157 0.171 0.18387 0.1948 RANDOM 20.871
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] 0.41 0.97 0.08 0.44 0.21 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.308 r_dihedral_angle_4_deg 21.82 r_dihedral_angle_3_deg 13.474 r_dihedral_angle_1_deg 7.079 r_long_range_B_refined 6.074 r_long_range_B_other 5.864 r_scangle_other 4.343 r_scbond_other 2.895 r_scbond_it 2.893 r_mcangle_other 2.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.308 r_dihedral_angle_4_deg 21.82 r_dihedral_angle_3_deg 13.474 r_dihedral_angle_1_deg 7.079 r_long_range_B_refined 6.074 r_long_range_B_other 5.864 r_scangle_other 4.343 r_scbond_other 2.895 r_scbond_it 2.893 r_mcangle_other 2.817 r_mcangle_it 2.816 r_mcbond_it 2.012 r_mcbond_other 2.009 r_angle_refined_deg 1.748 r_angle_other_deg 1.477 r_chiral_restr 0.087 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 2770 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing