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2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 Protein: 8.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 1mM Zn, 1mM Mn
Screen: Classics II (F10), 0.2M Sodium chloride, 0.1M BIS-TRIS pH 5.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.857 α = 90 b = 148.19 β = 90 c = 165.01 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 CCD MARMOSAIC 300 mm CCD C(111) 2019-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.6 30 100 0.136 0.136 0.149 0.059 14.4 6.2 85965 -3 38.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 100 0.79 0.79 0.861 0.341 0.837 2.5 6.3
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 6OAD 2.61 29.76 81597 4240 99.56 0.18411 0.1813 0.1869 0.2376 0.2373 RANDOM 41.039
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] 3.14 1.36 -4.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.819 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_4_deg 10.238 r_dihedral_angle_1_deg 4.224 r_long_range_B_refined 3.245 r_long_range_B_other 3.212 r_scangle_other 1.796 r_mcangle_it 1.708 r_mcangle_other 1.708 r_scbond_it 1.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.819 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_4_deg 10.238 r_dihedral_angle_1_deg 4.224 r_long_range_B_refined 3.245 r_long_range_B_other 3.212 r_scangle_other 1.796 r_mcangle_it 1.708 r_mcangle_other 1.708 r_scbond_it 1.112 r_scbond_other 1.111 r_angle_refined_deg 1.042 r_mcbond_it 0.99 r_mcbond_other 0.99 r_angle_other_deg 0.291 r_gen_planes_refined 0.052 r_gen_planes_other 0.047 r_chiral_restr 0.042 r_bond_refined_d 0.003 r_bond_other_d 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 19510 Nucleic Acid Atoms Solvent Atoms 614 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing