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Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 3'-sialyl-N-acetyllactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JH1 PDB ENTRY 2JH1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 VAPOUR DIFFUSION IN HANGING DROP 3.4 M AMMONIUM ACETATE 100 MM BIS-TRIS-PROPANE PH 7.0
Crystal Properties Matthews coefficient Solvent content 3.48 64.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.132 α = 90 b = 66.132 β = 90 c = 172.681 γ = 90
Symmetry Space Group P 43 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 CCD COLLIMATOR, MONOCHROMATOR, MIRROR 2006-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
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 18 100 0.09 38 7.6 17796 -3.7
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 99.9 0.41 6.7 7.8
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 2JH1 2.3 17.5 16806 915 100 0.175 0.173 0.1749 0.213 0.2106 RANDOM 35.84
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 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.783 r_dihedral_angle_3_deg 15.771 r_dihedral_angle_4_deg 10.247 r_dihedral_angle_1_deg 6.929 r_scangle_it 4.787 r_scbond_it 3.184 r_mcangle_it 2.143 r_angle_refined_deg 1.885 r_mcbond_it 1.373 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.783 r_dihedral_angle_3_deg 15.771 r_dihedral_angle_4_deg 10.247 r_dihedral_angle_1_deg 6.929 r_scangle_it 4.787 r_scbond_it 3.184 r_mcangle_it 2.143 r_angle_refined_deg 1.885 r_mcbond_it 1.373 r_nbtor_refined 0.301 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.188 r_symmetry_vdw_refined 0.183 r_chiral_restr 0.132 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 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_mcangle_other r_scbond_other 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 1719 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing