4ODI

2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 from Toxoplasma gondii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XQ9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295Protein - 7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3, Screen - Classics II (G12), 0.2M Magnesium chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0539.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.182α = 90
b = 149.474β = 90
c = 72.12γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lenses2013-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.6301000.1060.10618.37.33303333033-352
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)
12.62.641000.6450.6453.37.41604

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 REPLACEMENTTHROUGHOUT1XQ92.629.723131731317167199.770.199250.199250.197170.23881RANDOM56.296
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]
-1.482.24-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.112
r_dihedral_angle_3_deg11.868
r_dihedral_angle_4_deg11.554
r_long_range_B_refined6.815
r_long_range_B_other6.815
r_scangle_other4.75
r_mcangle_other3.542
r_mcangle_it3.541
r_scbond_it3.003
r_scbond_other3.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.112
r_dihedral_angle_3_deg11.868
r_dihedral_angle_4_deg11.554
r_long_range_B_refined6.815
r_long_range_B_other6.815
r_scangle_other4.75
r_mcangle_other3.542
r_mcangle_it3.541
r_scbond_it3.003
r_scbond_other3.003
r_dihedral_angle_1_deg2.382
r_mcbond_it2.268
r_mcbond_other2.255
r_angle_refined_deg1.626
r_angle_other_deg1.217
r_chiral_restr0.092
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7719
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms4

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling