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Crystal structure of Toxoplasma gondii sporozoite AMA1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X2Z PDB ENTRY 2X2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.0 M SUCCINIC ACID PH 7.0, 100 MM HEPES PH 7.0, 1% PEG MONOMETHYL ETHER 2000 AND 100 MM GLYCINE
Crystal Properties Matthews coefficient Solvent content 4.9 74.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.19 α = 90 b = 155.52 β = 92.31 c = 180.59 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 325 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 2.35 79.3 95.4 0.08 10 3.6 391285 2
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 2.35 2.48 75.8 0.34 2.1 2.4
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 2X2Z 2.35 78.04 387902 20508 99.52 0.21044 0.20869 0.2025 0.24393 0.2359 RANDOM 41.013
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] -0.06 -0.01 0.16 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.517 r_dihedral_angle_3_deg 19.655 r_dihedral_angle_4_deg 19.142 r_dihedral_angle_1_deg 8.303 r_angle_refined_deg 1.31 r_chiral_restr 0.111 r_gen_planes_refined 0.018 r_bond_refined_d 0.013 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.517 r_dihedral_angle_3_deg 19.655 r_dihedral_angle_4_deg 19.142 r_dihedral_angle_1_deg 8.303 r_angle_refined_deg 1.31 r_chiral_restr 0.111 r_gen_planes_refined 0.018 r_bond_refined_d 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it 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 34720 Nucleic Acid Atoms Solvent Atoms 1695 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing