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Crystal Structure of E. coli Aminopeptidase N in complex with L-Leucine
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 3.58 65.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.299 α = 90 b = 120.299 β = 90 c = 169.601 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++ 2015-01-01 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 20 95.6 0.1 13.85 5.3 107630
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 2.22 97.1 2.25 2.4
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 13.43 89668 4720 98.06 0.12636 0.12432 0.1393 0.16531 0.1735 RANDOM 22.7
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 37.092 r_dihedral_angle_4_deg 16.569 r_dihedral_angle_3_deg 12.494 r_long_range_B_refined 7.529 r_long_range_B_other 7.025 r_dihedral_angle_1_deg 6.187 r_scangle_other 5.368 r_scbond_it 3.638 r_scbond_other 3.607 r_mcangle_it 2.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.092 r_dihedral_angle_4_deg 16.569 r_dihedral_angle_3_deg 12.494 r_long_range_B_refined 7.529 r_long_range_B_other 7.025 r_dihedral_angle_1_deg 6.187 r_scangle_other 5.368 r_scbond_it 3.638 r_scbond_other 3.607 r_mcangle_it 2.436 r_mcangle_other 2.436 r_angle_refined_deg 1.983 r_mcbond_other 1.961 r_mcbond_it 1.96 r_angle_other_deg 1.091 r_chiral_restr 0.135 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 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 6940 Nucleic Acid Atoms Solvent Atoms 1214 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing