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Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 3'SiaLacNAc1-3
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 3.46 64.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.226 α = 90 b = 66.226 β = 90 c = 172.188 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 33.17 99.3 0.074 11.2 3.5 23609 23.545
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 2.11 100 0.2228 4.7 3.6 3837
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 27.75 23609 2626 97.94 0.16737 0.16501 0.1855 0.18875 0.2004 RANDOM 21.913
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] 0.14 0.14 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.665 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_4_deg 9.557 r_dihedral_angle_1_deg 6.341 r_scangle_it 3.548 r_scbond_it 2.324 r_angle_refined_deg 1.379 r_mcangle_it 1.23 r_mcbond_it 0.871 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.665 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_4_deg 9.557 r_dihedral_angle_1_deg 6.341 r_scangle_it 3.548 r_scbond_it 2.324 r_angle_refined_deg 1.379 r_mcangle_it 1.23 r_mcbond_it 0.871 r_nbtor_refined 0.301 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1737 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 109
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling