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Crystal Structure of Met260Ala mutant of E. coli Aminopeptidase N in complex with L-Phenylalanine
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 298 Sodium malonate
Crystal Properties Matthews coefficient Solvent content 3.65 66.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.033 α = 90 b = 121.033 β = 90 c = 170.808 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++ 2014-03-01 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 2.66 20 98.7 0.17 7.39 5.6 45125
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 2.66 2.75 96.7 2.43 5.3
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 2HPO 2.66 17.97 38723 2067 96.57 0.1428 0.13968 0.1492 0.20224 0.2065 RANDOM 21.857
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.005 r_dihedral_angle_4_deg 17.753 r_dihedral_angle_3_deg 16.272 r_dihedral_angle_1_deg 6.984 r_long_range_B_refined 5.449 r_long_range_B_other 5.428 r_scangle_other 3.865 r_scbond_it 2.403 r_scbond_other 2.383 r_mcangle_it 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.005 r_dihedral_angle_4_deg 17.753 r_dihedral_angle_3_deg 16.272 r_dihedral_angle_1_deg 6.984 r_long_range_B_refined 5.449 r_long_range_B_other 5.428 r_scangle_other 3.865 r_scbond_it 2.403 r_scbond_other 2.383 r_mcangle_it 2.21 r_mcangle_other 2.21 r_angle_refined_deg 1.746 r_mcbond_it 1.345 r_mcbond_other 1.343 r_angle_other_deg 0.855 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 6937 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing