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Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 2F-3'SiaLacNAc
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 7.6 290 3.6M Ammonium acetate, 100mM Bis/tris-propane, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.48 64.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.361 α = 90 b = 66.361 β = 90 c = 172.371 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 QUANTUM 4 mirrors 2007-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.934 ESRF BM14
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 29.68 98.9 0.075 12.7 3.7 26571 24.021
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 2.11 98.8 0.246 4.6 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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2JH1 2 29.68 26571 23882 2663 98.61 0.17024 0.16783 0.19114 0.2108 RANDOM 19.551
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] 0.1 0.1 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.208 r_dihedral_angle_3_deg 13.55 r_dihedral_angle_1_deg 8.252 r_dihedral_angle_4_deg 7.482 r_scangle_it 3.52 r_scbond_it 2.377 r_angle_refined_deg 1.428 r_mcangle_it 1.278 r_mcbond_it 0.903 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.208 r_dihedral_angle_3_deg 13.55 r_dihedral_angle_1_deg 8.252 r_dihedral_angle_4_deg 7.482 r_scangle_it 3.52 r_scbond_it 2.377 r_angle_refined_deg 1.428 r_mcangle_it 1.278 r_mcbond_it 0.903 r_nbtor_refined 0.301 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.108 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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 1750 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 95
Software Software Software Name Purpose ADSC Quantum data collection PHASER phasing REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling