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Plasmodium falciparum apical membrane antigen 3D7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 Crystals of PfAMA1-3D7 were obtained by mixing 1.2 micro-L of protein and 1.2 micro-L of reservoir buffer containing 12% PEG 3350, 0.1M Hepes pH 7 and 10% propanol-2. The final protein concentration was 3.5 mg/ml. Before mounting, 1 micro-L of a 20mM solution of a small molecule NCGC00015280 (demonstrated as inhibiting the AMA1-RON2 interaction and referenced as B43 in the PDB), was dissolved in DMSO and half diluted with the reservoir buffer, then added to the drop containing the crystals. Cryo-protecting buffer for the PfAMA1-3D7 crystals consisted of 90% of reservoir buffer containing 20% PEG 3350, 0.1M Hepes pH 7 and 10% propanol-2 supplemented with 10% glycerol, and 10% of a 20mM solution of B43.
Crystal Properties Matthews coefficient Solvent content 2.03 39.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.23 α = 89.13 b = 62.06 β = 89.9 c = 71.5 γ = 83.92
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
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 2.1 47.06 97.9 0.199 0.268 0.179 0.902 4.3 2 37352
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 2.1 2.21 0.872 1.183 0.795 0.215 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 46.37 35400 1908 97.77 0.20977 0.20732 0.2157 0.25599 0.2675 RANDOM 26.81
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] -0.44 -0.47 0.23 1.48 -1.01 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.346 r_dihedral_angle_2_deg 7.741 r_dihedral_angle_1_deg 7.041 r_long_range_B_refined 6.037 r_long_range_B_other 5.992 r_scangle_other 4.054 r_mcangle_it 3.719 r_mcangle_other 3.718 r_scbond_it 2.439 r_scbond_other 2.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.346 r_dihedral_angle_2_deg 7.741 r_dihedral_angle_1_deg 7.041 r_long_range_B_refined 6.037 r_long_range_B_other 5.992 r_scangle_other 4.054 r_mcangle_it 3.719 r_mcangle_other 3.718 r_scbond_it 2.439 r_scbond_other 2.439 r_mcbond_it 2.305 r_mcbond_other 2.304 r_angle_refined_deg 1.729 r_angle_other_deg 0.727 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_dihedral_angle_4_deg 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 4778 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing