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Crystal structure of aminopeptidase N from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-L7N655
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 25% PEG3350, 0.2M (NH4)2SO4, 0.1M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.43 49.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 283.588 α = 90 b = 56.747 β = 97.88 c = 58.138 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 16M 2020-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.2 50 81 0.036000000000000004 0.043 0.9990000000000001 16.15 3.2 231776
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.27 0.405 0.5589999999999999 0.708
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 1.45 140.45 151225 7976 97.57 0.1439 0.14273 0.1428 0.16616 0.1656 RANDOM 15.182
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] -0.48 0.3 0.26 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.566 r_dihedral_angle_4_deg 19.14 r_dihedral_angle_3_deg 11.931 r_dihedral_angle_1_deg 6.638 r_long_range_B_refined 6.356 r_long_range_B_other 5.902 r_scangle_other 3.557 r_scbond_it 2.343 r_scbond_other 2.337 r_angle_refined_deg 1.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.566 r_dihedral_angle_4_deg 19.14 r_dihedral_angle_3_deg 11.931 r_dihedral_angle_1_deg 6.638 r_long_range_B_refined 6.356 r_long_range_B_other 5.902 r_scangle_other 3.557 r_scbond_it 2.343 r_scbond_other 2.337 r_angle_refined_deg 1.851 r_mcangle_other 1.8 r_mcangle_it 1.798 r_angle_other_deg 1.616 r_mcbond_it 1.271 r_mcbond_other 1.269 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 6645 Nucleic Acid Atoms Solvent Atoms 1060 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing