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Crystal Structure of Lopinavir bound Plasmepsin II (PMII) from Plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 1.4 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.81 56.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.94 α = 90 b = 108.94 β = 90 c = 70.2 γ = 90
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++ 2020-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 3.2 38.52 99.9 0.99 9.95 7.54 6877 87.22
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 3.2 3.3 100 0.37 1.04 7.57
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5YIC 3.2 38.52 6531 344 99.85 0.2268 0.22459 0.2224 0.26617 0.2703 RANDOM 127.423
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] 5.26 5.26 -10.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.217 r_dihedral_angle_3_deg 20.908 r_dihedral_angle_4_deg 12.205 r_dihedral_angle_1_deg 9.262 r_long_range_B_other 6.985 r_long_range_B_refined 6.984 r_scangle_other 2.724 r_mcangle_it 2.423 r_mcangle_other 2.423 r_scbond_it 1.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.217 r_dihedral_angle_3_deg 20.908 r_dihedral_angle_4_deg 12.205 r_dihedral_angle_1_deg 9.262 r_long_range_B_other 6.985 r_long_range_B_refined 6.984 r_scangle_other 2.724 r_mcangle_it 2.423 r_mcangle_other 2.423 r_scbond_it 1.526 r_scbond_other 1.522 r_angle_refined_deg 1.437 r_mcbond_it 1.37 r_mcbond_other 1.37 r_angle_other_deg 1.1 r_chiral_restr 0.057 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2606 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing