2JHD

Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 3'-sialyl-N-acetyllactosamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JH1PDB ENTRY 2JH1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7VAPOUR DIFFUSION IN HANGING DROP 3.4 M AMMONIUM ACETATE 100 MM BIS-TRIS-PROPANE PH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.4864.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.132α = 90
b = 66.132β = 90
c = 172.681γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDCOLLIMATOR, MONOCHROMATOR, MIRROR2006-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.1SRSPX14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.3181000.09387.617796-3.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3899.90.416.77.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2JH12.317.5168069151000.1750.1730.213RANDOM35.84
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]
-0.01-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.783
r_dihedral_angle_3_deg15.771
r_dihedral_angle_4_deg10.247
r_dihedral_angle_1_deg6.929
r_scangle_it4.787
r_scbond_it3.184
r_mcangle_it2.143
r_angle_refined_deg1.885
r_mcbond_it1.373
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.783
r_dihedral_angle_3_deg15.771
r_dihedral_angle_4_deg10.247
r_dihedral_angle_1_deg6.929
r_scangle_it4.787
r_scbond_it3.184
r_mcangle_it2.143
r_angle_refined_deg1.885
r_mcbond_it1.373
r_nbtor_refined0.301
r_nbd_refined0.219
r_symmetry_hbond_refined0.192
r_xyhbond_nbd_refined0.188
r_symmetry_vdw_refined0.183
r_chiral_restr0.132
r_bond_refined_d0.023
r_gen_planes_refined0.009
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 AtomsNumber
Protein Atoms1719
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing