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Crystal structure of Aminopeptidase N in complex with 2,4-diaminobutyric 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 2.0M malonic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.53 65.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.601 α = 90 b = 120.601 β = 90 c = 170.479 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) 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 2.3 50 98 0.11 0.087 79.1 5.7 63115 63115
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 2.3 2.38 92.2 0.437 0.591 12.1 3.4 5880
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2.3 49.94 63115 61036 1908 97.58 0.15585 0.15449 0.1544 0.19838 0.1941 RANDOM 30.331
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] 0.63 0.31 0.63 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.754 r_dihedral_angle_4_deg 21.406 r_dihedral_angle_3_deg 15.168 r_dihedral_angle_1_deg 6.44 r_scangle_it 6.078 r_scbond_it 3.857 r_mcangle_it 2.054 r_angle_refined_deg 1.997 r_mcbond_it 1.057 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.754 r_dihedral_angle_4_deg 21.406 r_dihedral_angle_3_deg 15.168 r_dihedral_angle_1_deg 6.44 r_scangle_it 6.078 r_scbond_it 3.857 r_mcangle_it 2.054 r_angle_refined_deg 1.997 r_mcbond_it 1.057 r_chiral_restr 0.126 r_bond_refined_d 0.024 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6940 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 86
Software Software Software Name Purpose APEX data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling