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Structure of Plasmepsin X (PM10, PMX) from Plasmodium falciparum 3D7 in complex with UCB7362
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RY7 apo structure 7ry7, minus pro domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.4 290 RigakuReagents JCSG A7 optimization screen: 100mM Tris HCl / NaOH pH 9.4, 17.86% PEG 8000: PlfaA.17789.b.HE11.PD38363 at 11.4mg/ml: cryo: 20% EG: tray: 3908603 D3: puck qpu2-2
Crystal Properties Matthews coefficient Solvent content 2.31 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.71 α = 90 b = 61.43 β = 90.769 c = 143.98 γ = 90
Symmetry Space Group P 1 21 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 CCD RAYONIX MX-300 2019-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.85 50 99.6 0.069 0.082 0.998 12.66 3.683 22559 68.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.92 99.8 0.562 0.656 0.913 2.11 3.797
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE apo structure 7ry7, minus pro domain 2.85 47.99 1.35 22495 2027 99.38 0.2385 0.2344 0.2336 0.28 0.2785 0 78.08
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 13.5571 f_angle_d 0.5673 f_chiral_restr 0.0486 f_plane_restr 0.004 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4989 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 66
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing