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Crystal Structure of E. coli Aminopeptidase N in complex with Lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HPO PDB entry 2HPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 2.0 M Sodium malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.52 65.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.561 α = 90 b = 120.561 β = 90 c = 170.269 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 CCD ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2007-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.5 50 88.8 0.092 13.4 5.3 201760 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 48.6 0.532 3.5 10919
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 PDB entry 2HPO 1.5 49.94 201607 6049 88.84 0.147 0.147 0.1453 0.165 0.1631 RANDOM 17.636
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] -0.09 -0.05 -0.09 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.529 r_dihedral_angle_4_deg 17.248 r_dihedral_angle_3_deg 12.034 r_dihedral_angle_1_deg 5.427 r_scangle_it 3.439 r_scbond_it 2.182 r_mcangle_it 1.291 r_angle_refined_deg 1.12 r_mcbond_it 0.743 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.529 r_dihedral_angle_4_deg 17.248 r_dihedral_angle_3_deg 12.034 r_dihedral_angle_1_deg 5.427 r_scangle_it 3.439 r_scbond_it 2.182 r_mcangle_it 1.291 r_angle_refined_deg 1.12 r_mcbond_it 0.743 r_nbtor_refined 0.302 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.191 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.078 r_metal_ion_refined 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6940 Nucleic Acid Atoms Solvent Atoms 1216 Heterogen Atoms 88
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection HKL-2000 data reduction