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Structure of the malaria antigen AMA1 in complex with a growth-inhibitory antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z40 1Z40, 2CGR experimental model PDB 2CGR 1Z40, 2CGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 20 mM MES, 10 mM MnCl2, 6 % PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.54 51.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.905 α = 90 b = 51.487 β = 108.49 c = 95.257 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 IMAGE PLATE RIGAKU RAXIS IV++ Osmic multilayer mirrors 2004-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 30 99.5 0.057 14 3.7 36116 36116 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 98.4 0.29 4 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1Z40, 2CGR 2.3 27.95 36116 36116 1899 100 0.21152 0.21152 0.20914 0.2023 0.25565 0.2473 RANDOM 36.36
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] -2.51 -0.68 1.29 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.37 r_dihedral_angle_4_deg 17.465 r_dihedral_angle_3_deg 15.476 r_dihedral_angle_1_deg 5.814 r_scangle_it 1.481 r_angle_refined_deg 1.07 r_scbond_it 0.915 r_mcangle_it 0.636 r_mcbond_it 0.358 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.37 r_dihedral_angle_4_deg 17.465 r_dihedral_angle_3_deg 15.476 r_dihedral_angle_1_deg 5.814 r_scangle_it 1.481 r_angle_refined_deg 1.07 r_scbond_it 0.915 r_mcangle_it 0.636 r_mcbond_it 0.358 r_nbtor_refined 0.299 r_nbd_refined 0.176 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.092 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5378 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling PHASER phasing