☰ Navigation Tabs
Crystal Structure of E. coli Aminopeptidase N in complex with L-2,3-Diaminopropionic 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 3.62 66.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.69 α = 90 b = 120.69 β = 90 c = 170.46 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++ 2014-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54179
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 2.22 49.25 99.5 0.18 5.31 5 70135
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 2.22 2.35 99 2.78 4.8
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 2.22 49.25 66428 3535 98.27 0.2013 0.19892 0.24589 0.2117 RANDOM 21.283
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 37.807 r_dihedral_angle_4_deg 19.109 r_dihedral_angle_3_deg 15.104 r_dihedral_angle_1_deg 6.459 r_long_range_B_refined 5.159 r_long_range_B_other 5.062 r_scangle_other 3.401 r_scbond_it 2.094 r_scbond_other 2.09 r_mcangle_it 1.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.807 r_dihedral_angle_4_deg 19.109 r_dihedral_angle_3_deg 15.104 r_dihedral_angle_1_deg 6.459 r_long_range_B_refined 5.159 r_long_range_B_other 5.062 r_scangle_other 3.401 r_scbond_it 2.094 r_scbond_other 2.09 r_mcangle_it 1.932 r_mcangle_other 1.932 r_angle_refined_deg 1.648 r_mcbond_it 1.169 r_mcbond_other 1.168 r_angle_other_deg 0.829 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 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 6940 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing