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Plasmodium falciparum Aminopeptidase P in complex with hydroxamic-peptide based inhibitor 6e
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289.15 0.1M Tris pH 8.5, 22% v/v PEG smear broad (4.55% v/v PEG 400, 4.55% v/v PEG 500 MME, 4.55% v/v PEG 600, 4.55% w/v PEG 1000, 4.55% w/v PEG 2000, 4.55% w/v PEG 3350, 4.55% w/v PEG 4000, 4.55% w/v PEG 5000 MME, 4.55% w/v PEG 6000, 4.55% w/v PEG 8000, 4.55% w/v PEG 10000).
Crystal Properties Matthews coefficient Solvent content 2.38 48.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.516 α = 90 b = 96.878 β = 106.287 c = 109.237 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS EIGER2 XE 16M 2022-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 104.85 100 0.993 6 13.9 39892
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.81 0.662
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.7 104.853 39889 1970 100 0.208 0.2065 0.2102 0.2436 0.2179 RANDOM 70.815
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] -4.251 -1.805 0.186 4.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.521 r_dihedral_angle_6_deg 13.799 r_dihedral_angle_2_deg 9.043 r_dihedral_angle_1_deg 7.417 r_lrange_it 6.557 r_lrange_other 6.556 r_mcangle_it 4.667 r_mcangle_other 4.667 r_scangle_it 4.62 r_scangle_other 4.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.521 r_dihedral_angle_6_deg 13.799 r_dihedral_angle_2_deg 9.043 r_dihedral_angle_1_deg 7.417 r_lrange_it 6.557 r_lrange_other 6.556 r_mcangle_it 4.667 r_mcangle_other 4.667 r_scangle_it 4.62 r_scangle_other 4.619 r_mcbond_it 2.882 r_mcbond_other 2.879 r_scbond_it 2.868 r_scbond_other 2.867 r_angle_refined_deg 1.401 r_dihedral_angle_other_2_deg 0.925 r_angle_other_deg 0.475 r_nbd_refined 0.212 r_symmetry_nbd_other 0.196 r_nbd_other 0.193 r_nbtor_refined 0.182 r_symmetry_nbd_refined 0.162 r_xyhbond_nbd_refined 0.138 r_ncsr_local_group_1 0.123 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_refined 0.069 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10429 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing