4IR8

1.85 Angstrom Crystal Structure of Putative Sedoheptulose-1,7 bisphosphatase from Toxoplasma gondii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KBZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6295Protein: 20.0mG/mL, 0.5M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: PEG's (A2), 0.1M Sodium acetate (pH 4.6), 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3447.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.4α = 90
b = 64.4β = 90
c = 591.61γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMirrors2011-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97903APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.853099.40.08829.614.36433664336-323.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8899.30.6065.3153115

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3KBZ1.8529.526104061040324299.60.15580.15580.154250.18465RANDOM20.557
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]
0.590.290.59-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.954
r_dihedral_angle_4_deg12.809
r_dihedral_angle_3_deg9.449
r_scangle_it4.359
r_dihedral_angle_1_deg3.278
r_scbond_it2.715
r_mcangle_it1.676
r_angle_refined_deg1.323
r_mcbond_it0.966
r_angle_other_deg0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.954
r_dihedral_angle_4_deg12.809
r_dihedral_angle_3_deg9.449
r_scangle_it4.359
r_dihedral_angle_1_deg3.278
r_scbond_it2.715
r_mcangle_it1.676
r_angle_refined_deg1.323
r_mcbond_it0.966
r_angle_other_deg0.83
r_mcbond_other0.304
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4828
Nucleic Acid Atoms
Solvent Atoms540
Heterogen Atoms32

Software

Software
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing