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Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(2-chlorobenzyl)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, pH 8.5, 0.2M Magnesium chloride, 24% PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.275 α = 90 b = 109.254 β = 90 c = 111.884 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 2016-06-03 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) 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 1.81 23.71 99.9 0.05 0.055 0.022 0.998 25.6 6 83333 25.28
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 1.81 1.87 100 0.21 0.231 0.095 0.984 8.11 5.8
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 1.81 23.71 78262 4002 98.43 0.1716 0.1695 0.1799 0.213 0.22 RANDOM 27.482
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 37.56 r_dihedral_angle_4_deg 18.168 r_dihedral_angle_3_deg 13.438 r_dihedral_angle_1_deg 6.391 r_angle_refined_deg 1.881 r_angle_other_deg 1.078 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.56 r_dihedral_angle_4_deg 18.168 r_dihedral_angle_3_deg 13.438 r_dihedral_angle_1_deg 6.391 r_angle_refined_deg 1.881 r_angle_other_deg 1.078 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7308 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 61
Software Software Software Name Purpose DENZO data collection SCALEPACK data scaling MOLREP model building REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction