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Crystal structure of E.coli aminopeptidase N in complex with Puromycin aminonucleoside
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 7.5 298 2.0M Sodium malonate
Crystal Properties Matthews coefficient Solvent content 3.5 64.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.223 α = 90 b = 120.223 β = 90 c = 170.124 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++ 2016-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 50 99.9 0.044 0.049 0.021 19.6 5.6 186872
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 100 0.324 0.358 0.152 0.94 5.4
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 2HPO 1.6 50 176842 9525 99.7 0.1579 0.1567 0.1707 0.1789 0.1894 RANDOM 24.334
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 37.153 r_dihedral_angle_4_deg 17.605 r_dihedral_angle_3_deg 13.007 r_dihedral_angle_1_deg 6.012 r_angle_refined_deg 2.509 r_angle_other_deg 1.961 r_chiral_restr 0.17 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.153 r_dihedral_angle_4_deg 17.605 r_dihedral_angle_3_deg 13.007 r_dihedral_angle_1_deg 6.012 r_angle_refined_deg 2.509 r_angle_other_deg 1.961 r_chiral_restr 0.17 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6940 Nucleic Acid Atoms Solvent Atoms 806 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement DENZO data collection SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction Coot model building HKL-2000 data reduction