3F5E

Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 2'F-3'SiaLacNAc1-3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.62903.6M Ammonium acetate, 100mM Bis/tris-propane, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.4764.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.325α = 90
b = 66.325β = 90
c = 172.091γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2007-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.934ESRFBM14

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
1231.7399.40.07610.73.92398622.268
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)
122.111000.2225.63.93769

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 2JH1229.6623986267599.270.16870.164970.2035RANDOM22.106
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]
0.120.12-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.827
r_dihedral_angle_3_deg13.592
r_dihedral_angle_4_deg8.938
r_dihedral_angle_1_deg6.263
r_scangle_it3.706
r_scbond_it2.516
r_angle_refined_deg1.355
r_mcangle_it1.242
r_mcbond_it0.861
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.827
r_dihedral_angle_3_deg13.592
r_dihedral_angle_4_deg8.938
r_dihedral_angle_1_deg6.263
r_scangle_it3.706
r_scbond_it2.516
r_angle_refined_deg1.355
r_mcangle_it1.242
r_mcbond_it0.861
r_nbtor_refined0.301
r_nbd_refined0.202
r_symmetry_vdw_refined0.175
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.126
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms1740
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms109

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling