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Crystal structure of E. coli Aminopeptidase N in complex with arginine
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 1.8 M Sodium malonate pH=7/0, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.49 64.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.204 α = 90 b = 120.204 β = 90 c = 169.655 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 1.0000 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 50 99.9 0.1 0.08 13.2 5.6 95605 95605 2 2 22.885
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.4 0.57 0.5 2.4 5 9360
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 44.37 20 2 95736 92657 2855 99.77 0.15448 0.15343 0.1554 0.18846 0.1891 RANDOM 20.646
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 36.97 r_dihedral_angle_4_deg 18.644 r_dihedral_angle_3_deg 14.035 r_dihedral_angle_1_deg 6.017 r_scangle_it 4.185 r_scbond_it 2.53 r_angle_refined_deg 1.434 r_mcangle_it 1.393 r_mcbond_it 0.731 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.97 r_dihedral_angle_4_deg 18.644 r_dihedral_angle_3_deg 14.035 r_dihedral_angle_1_deg 6.017 r_scangle_it 4.185 r_scbond_it 2.53 r_angle_refined_deg 1.434 r_mcangle_it 1.393 r_mcbond_it 0.731 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.239 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.184 r_metal_ion_refined 0.141 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6940 Nucleic Acid Atoms Solvent Atoms 765 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement APEX data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing