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Plasmodium falciparum M1 aminopeptidase (PfA-M1) bound to inhibitor 3k (MIPS3415)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20-30% poly(ethylene glycol) (PEG)8000, 0.1 M Tris pH 7.5-8.5, 0.2 M MgCl2, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 1.87 34.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.953 α = 90 b = 109.53 β = 90 c = 116.75 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 CCD ADSC QUANTUM 210r 2020-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 2.2 49.58 99.6 0.157 0.17 0.064 0.996 10.3 6.9 31.25
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 2.2 2.27 98.2 1.42 1.532 0.571 0.62 1.8 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 49.58 1.33 92643 4641 99.49 0.1968 0.1945 0.1983 0.2397 0.2412 46.74
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 f_dihedral_angle_d 7.3685 f_angle_d 0.5187 f_chiral_restr 0.0403 f_plane_restr 0.0043 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7132 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing