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Crystal Structure of Ritonavir 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 7 293 2.5 M sodium formate, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.29 α = 90 b = 70.41 β = 133.61 c = 106.67 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 CCD RAYONIX MX225HE 2019-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.9795 RRCAT INDUS-2 PX-BL21
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 1.9 39.89 95.9 0.99 16.16 2.89 61329 41.24
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 1.9 2 96.6 0.65 1.84 2.73
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5YIC 1.9 39.89 58262 3067 96.34 0.22448 0.22225 0.26126 0.2505 RANDOM 51.907
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] 1.55 1.21 -5.03 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.682 r_dihedral_angle_4_deg 21.774 r_dihedral_angle_3_deg 14.629 r_long_range_B_refined 7.676 r_long_range_B_other 7.659 r_dihedral_angle_1_deg 7.502 r_angle_refined_deg 1.309 r_angle_other_deg 1.08 r_scangle_other 0.985 r_mcangle_it 0.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.682 r_dihedral_angle_4_deg 21.774 r_dihedral_angle_3_deg 14.629 r_long_range_B_refined 7.676 r_long_range_B_other 7.659 r_dihedral_angle_1_deg 7.502 r_angle_refined_deg 1.309 r_angle_other_deg 1.08 r_scangle_other 0.985 r_mcangle_it 0.722 r_mcangle_other 0.722 r_scbond_it 0.586 r_scbond_other 0.586 r_mcbond_it 0.405 r_mcbond_other 0.405 r_chiral_restr 0.045 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5189 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 567
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing