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Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(2,4-difluorobenzyl)ureido)-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, HANGING DROP 8.5 298 0.1M Tris pH8.5, 0.2M magnesium chloride, 24%PEG2000
Crystal Properties Matthews coefficient Solvent content 2.21 44.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.564 α = 90 b = 109.241 β = 90 c = 112.518 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 2016-05-28 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 1.73 24.66 99.9 0.046 0.999 41 14.1 96409 19.4
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 1.73 1.79 100 0.105 0.995 16.28 13.6
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 4X2U 1.73 24.66 90642 4826 98.98 0.1632 0.1613 0.1745 0.2013 0.2098 RANDOM 20.687
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 35.99 r_dihedral_angle_4_deg 16.572 r_dihedral_angle_3_deg 12.994 r_dihedral_angle_1_deg 6.239 r_angle_refined_deg 1.992 r_angle_other_deg 1.107 r_chiral_restr 0.131 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.99 r_dihedral_angle_4_deg 16.572 r_dihedral_angle_3_deg 12.994 r_dihedral_angle_1_deg 6.239 r_angle_refined_deg 1.992 r_angle_other_deg 1.107 r_chiral_restr 0.131 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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 561 Heterogen Atoms 44
Software Software Software Name Purpose DENZO data collection SCALEPACK data scaling MOLREP model building REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction