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Plasmodium falciparum Aminopeptidase P in complex with hydroxamic-peptide based inhibitor 6d
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 7.5 289.15 0.1 M HEPES, pH 7.5, 25% v/v PEG smear medium (12.5% w/v PEG 3350, 12.5% w/v PEG 4000, 12.5% w/v PEG 2000, 12.5% w/v PEG 5000 MME)
Crystal Properties Matthews coefficient Solvent content 2.18 43.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.932 α = 90 b = 94.081 β = 105.494 c = 102.285 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 PILATUS3 6M 2021-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97950 Diamond I24
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 2.55 98.57 100 0.999 10.1 14.2 43296
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 2.55 2.65 0.525
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 2.55 98.568 43277 2111 99.956 0.222 0.2207 0.2221 0.2472 0.2278 RANDOM 80.95
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] -5.451 -1.467 3.503 2.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.296 r_dihedral_angle_6_deg 13.019 r_dihedral_angle_1_deg 6.231 r_dihedral_angle_2_deg 6.081 r_lrange_it 5.376 r_lrange_other 5.376 r_scangle_it 3.549 r_scangle_other 3.549 r_mcangle_it 3.37 r_mcangle_other 3.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.296 r_dihedral_angle_6_deg 13.019 r_dihedral_angle_1_deg 6.231 r_dihedral_angle_2_deg 6.081 r_lrange_it 5.376 r_lrange_other 5.376 r_scangle_it 3.549 r_scangle_other 3.549 r_mcangle_it 3.37 r_mcangle_other 3.37 r_scbond_it 2.137 r_scbond_other 2.131 r_mcbond_it 2.004 r_mcbond_other 2.004 r_angle_refined_deg 1.051 r_dihedral_angle_other_2_deg 0.651 r_angle_other_deg 0.384 r_symmetry_xyhbond_nbd_refined 0.25 r_symmetry_nbd_refined 0.238 r_nbd_other 0.191 r_nbd_refined 0.19 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.154 r_ncsr_local_group_1 0.121 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.056 r_chiral_restr 0.051 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10187 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing