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Three dimensional structure of plasmepsin II in complex with hydroxyethylamine-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BJU PDB ENTRY 2BJU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 0.1M CITRIC ACID, PH 4.5, 0.3M AMMONIUM ACETATE, 25% PEG 3350, PROTEIN 10 MG/ML, VAPOR DIFFUSION, SITTING DROP, TIME 2-4 WEEKS.
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.95 α = 90 b = 115.25 β = 110.75 c = 93.17 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 MARRESEARCH MIRRORS 2011-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 30 98 0.07 9.2 2.6 166099 16.852
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.95 99.4 0.28 3.5 2.5
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 PDB ENTRY 2BJU 1.85 29.98 157768 8325 97.87 0.1604 0.15783 0.168 0.2089 0.2141 RANDOM 24.732
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] 0.01 -0.02 -0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.071 r_dihedral_angle_4_deg 17.45 r_dihedral_angle_3_deg 14.193 r_dihedral_angle_1_deg 7.105 r_mcangle_it 3.589 r_scbond_it 3.282 r_mcbond_it 2.394 r_mcbond_other 2.389 r_angle_refined_deg 1.866 r_angle_other_deg 0.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.071 r_dihedral_angle_4_deg 17.45 r_dihedral_angle_3_deg 14.193 r_dihedral_angle_1_deg 7.105 r_mcangle_it 3.589 r_scbond_it 3.282 r_mcbond_it 2.394 r_mcbond_other 2.389 r_angle_refined_deg 1.866 r_angle_other_deg 0.877 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15308 Nucleic Acid Atoms Solvent Atoms 1189 Heterogen Atoms 294
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling