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Crystal Structure of Met260Ala mutant of E. coli Aminopeptidase N in complex with L-Alanine
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 3.6 65.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.538 α = 90 b = 120.538 β = 90 c = 170.207 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++ 2014-02-15 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 2.9 25 99.9 0.25 7 5.6 32062
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 2.9 3 99.9 2.58 5.6
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 2.91 24.92 30406 1622 99.74 0.14966 0.1465 0.1546 0.21021 0.2123 RANDOM 27.585
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 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.013 r_dihedral_angle_4_deg 19.277 r_dihedral_angle_3_deg 16.468 r_dihedral_angle_1_deg 6.506 r_long_range_B_other 5.806 r_long_range_B_refined 5.803 r_scangle_other 4.146 r_mcangle_it 2.58 r_mcangle_other 2.58 r_scbond_it 2.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.013 r_dihedral_angle_4_deg 19.277 r_dihedral_angle_3_deg 16.468 r_dihedral_angle_1_deg 6.506 r_long_range_B_other 5.806 r_long_range_B_refined 5.803 r_scangle_other 4.146 r_mcangle_it 2.58 r_mcangle_other 2.58 r_scbond_it 2.472 r_scbond_other 2.468 r_angle_refined_deg 1.644 r_mcbond_it 1.543 r_mcbond_other 1.543 r_angle_other_deg 0.982 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 195 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing