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Plasmodium vivax Apical Membrane Antigen 1/Fab complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W81 experimental model PDB 6YHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 290 Crystals were obtained by mixing 0.8 micro-L of PvAMA1-Fab complex with 0.2 micro-L of 15% 1,2,3 heptanetriol and 0.8 micro-L of reservoir buffer comprising 20% PEG 2000 monomethylether and 0.1 M Tris pH 7. The final protein concentration was 3.2 mg/ml.
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.39 α = 90 b = 214.68 β = 90 c = 57.41 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 210r 2006-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 3.05 73.39 99.9 0.167 0.181 0.067 0.996 11.8 7.1 18062
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 3.05 3.26 100 1.203 1.296 0.48 0.316 7.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.05 69.54 17069 946 99.87 0.22508 0.22134 0.29202 0.2631 RANDOM 95.223
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] -0.76 0.41 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.615 r_long_range_B_refined 8.205 r_long_range_B_other 8.205 r_dihedral_angle_1_deg 6.666 r_mcangle_other 5.818 r_mcangle_it 5.814 r_scangle_other 5.545 r_mcbond_it 3.616 r_mcbond_other 3.615 r_scbond_it 3.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.615 r_long_range_B_refined 8.205 r_long_range_B_other 8.205 r_dihedral_angle_1_deg 6.666 r_mcangle_other 5.818 r_mcangle_it 5.814 r_scangle_other 5.545 r_mcbond_it 3.616 r_mcbond_other 3.615 r_scbond_it 3.346 r_scbond_other 3.346 r_dihedral_angle_2_deg 3.302 r_angle_refined_deg 1.646 r_angle_other_deg 0.787 r_chiral_restr 0.086 r_bond_refined_d 0.021 r_bond_other_d 0.017 r_gen_planes_refined 0.007 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 6293 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing