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Crystal structure of E. coli Aminopeptidase N in complex with tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HPO PDB ID 2HPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 2M Sodium Malonate, pH=7.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.53 65.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.64 α = 90 b = 120.64 β = 90 c = 170.64 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) 2007-05-06 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 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 1.85 50 100 0.054 19.5 5.2 122655
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 100 0.39 2.9 5.2 12151
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 ID 2HPO 1.85 49.27 122587 6160 99.95 0.153 0.151 0.1509 0.178 0.1776 RANDOM 17.431
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 37.034 r_dihedral_angle_4_deg 17.314 r_dihedral_angle_3_deg 12.689 r_dihedral_angle_1_deg 5.685 r_scangle_it 3.635 r_scbond_it 2.13 r_angle_refined_deg 1.23 r_mcangle_it 1.18 r_mcbond_it 0.606 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.034 r_dihedral_angle_4_deg 17.314 r_dihedral_angle_3_deg 12.689 r_dihedral_angle_1_deg 5.685 r_scangle_it 3.635 r_scbond_it 2.13 r_angle_refined_deg 1.23 r_mcangle_it 1.18 r_mcbond_it 0.606 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.235 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.162 r_metal_ion_refined 0.109 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6940 Nucleic Acid Atoms Solvent Atoms 1004 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction BOS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing