3GG8 | pdb_00003gg8

Crystal structure of the Toxoplasma gondii Pyruvate Kinase N terminal truncated


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EOEPDB entry 3EOE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP75 % PEG 3350, 0.1 M Succinic Acid, pH 7.0, 3 mM Chembridge #5175181, 20% glycerol, Vapor diffusion, hanging drop
Crystal Properties
Matthews coefficientSolvent content
2.4449.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.023α = 90
b = 92.311β = 105.57
c = 112.443γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2008-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.25097.90.0880.0533.8108075105806
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2896.30.9130.91323.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3EOE2.2142.45108075100484526397.610.209230.206340.230.265160.28RANDOM35.302
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]
1.942.350.11-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.129
r_dihedral_angle_4_deg18.235
r_dihedral_angle_3_deg17.413
r_dihedral_angle_1_deg5.462
r_scangle_it2.111
r_scbond_it1.312
r_angle_refined_deg1.282
r_mcangle_it0.701
r_mcbond_it0.435
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.129
r_dihedral_angle_4_deg18.235
r_dihedral_angle_3_deg17.413
r_dihedral_angle_1_deg5.462
r_scangle_it2.111
r_scbond_it1.312
r_angle_refined_deg1.282
r_mcangle_it0.701
r_mcbond_it0.435
r_nbtor_refined0.296
r_symmetry_hbond_refined0.213
r_nbd_refined0.203
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.141
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.004
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 Atoms14240
Nucleic Acid Atoms
Solvent Atoms484
Heterogen Atoms16

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction