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Crystal Structure of Met260Ala mutant of E. coli Aminopeptidase N in complex with 2,4-diaminobutyric acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 Sodium malonate
Crystal Properties Matthews coefficient Solvent content 3.63 66.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.638 α = 90 b = 120.638 β = 90 c = 171.304 γ = 120
Symmetry Space Group P 31 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 100 IMAGE PLATE RIGAKU RAXIS IV++ 2014-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.15 20 100 0.13 11.98 4.8 78497
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 100 3.06 4.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2HPO 2.15 19.81 74313 3938 99.58 0.14511 0.14312 0.18144 0.1641 RANDOM 22.476
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.996 r_dihedral_angle_4_deg 18.021 r_dihedral_angle_3_deg 13.678 r_long_range_B_refined 6.47 r_dihedral_angle_1_deg 6.27 r_long_range_B_other 6.12 r_scangle_other 4.677 r_scbond_it 3.022 r_scbond_other 3.018 r_mcangle_it 2.483
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.996 r_dihedral_angle_4_deg 18.021 r_dihedral_angle_3_deg 13.678 r_long_range_B_refined 6.47 r_dihedral_angle_1_deg 6.27 r_long_range_B_other 6.12 r_scangle_other 4.677 r_scbond_it 3.022 r_scbond_other 3.018 r_mcangle_it 2.483 r_mcangle_other 2.483 r_angle_refined_deg 1.828 r_mcbond_it 1.707 r_mcbond_other 1.707 r_angle_other_deg 1.042 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6946 Nucleic Acid Atoms Solvent Atoms 1138 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing