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Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-((2S,3R)-3-amino-2-hydroxy-4-phenylbutanamido)- N-hydroxy-4-methylpentanamide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 0.1M Tris pH 8.5, 0.2M Magnesium chloride, 24% PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.22 44.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.988 α = 90 b = 109.258 β = 90 c = 112.238 γ = 90
Symmetry Space Group P 21 21 21
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 2016-05-26 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) CC (Half) 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 1.83 24.96 98.9 0.062 0.997 24.4 6.1 80888 27.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.896 99.8 0.064 0.963 5.79 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4X2U 1.83 24.96 76530 4044 98.39 0.168 0.1659 0.2073 0.2367 RANDOM 29.014
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 36.459 r_dihedral_angle_4_deg 15.991 r_dihedral_angle_3_deg 13.596 r_dihedral_angle_1_deg 6.247 r_angle_refined_deg 1.862 r_angle_other_deg 1.097 r_chiral_restr 0.138 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.459 r_dihedral_angle_4_deg 15.991 r_dihedral_angle_3_deg 13.596 r_dihedral_angle_1_deg 6.247 r_angle_refined_deg 1.862 r_angle_other_deg 1.097 r_chiral_restr 0.138 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7308 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 32
Software Software Software Name Purpose DENZO data collection SCALEPACK data scaling MOLREP model building REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction