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Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-N-hydroxy-4-methyl-2-(3-(3-methylbenzyl)ureido)pentanamide
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% PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.21 44.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.436 α = 90 b = 109.267 β = 90 c = 112.504 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++ 2016-06-04 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 1.73 25 99.6 0.032 0.035 0.014 42.4 6.3 95904
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 1.73 1.79 100 0.083 0.09 0.036 0.996 6.2
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 1.73 25 90688 4838 99.07 0.162 0.1602 0.1957 0.2349 RANDOM 18.647
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 36.284 r_dihedral_angle_4_deg 16.293 r_dihedral_angle_3_deg 13.251 r_dihedral_angle_1_deg 6.187 r_angle_refined_deg 2.01 r_angle_other_deg 1.096 r_chiral_restr 0.131 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.284 r_dihedral_angle_4_deg 16.293 r_dihedral_angle_3_deg 13.251 r_dihedral_angle_1_deg 6.187 r_angle_refined_deg 2.01 r_angle_other_deg 1.096 r_chiral_restr 0.131 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7308 Nucleic Acid Atoms Solvent Atoms 625 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement DENZO data collection SCALEPACK data scaling MOLREP model building PDB_EXTRACT data extraction DENZO data reduction