2Y61

Crystal structure of Leishmanial E65Q-TIM complexed with S-Glycidol phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N55PDB ENTRY 1N55

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.529321% PEG6000, 0.1 M SODIUM ACETATE PH 4.5-5.5, 1MM DTT, 1MM EDTA, 1MM NAN3
Crystal Properties
Matthews coefficientSolvent content
2.30.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.14α = 90
b = 52.47β = 117.85
c = 58.09γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X12EMBL/DESY, HAMBURGX12

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
10.991097.70.0721.45.5140160
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)
10.991.0295.30.443.84

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB ENTRY 1N550.9910133049700397.70.10570.1247RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
1941.652322.88
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.105
s_zero_chiral_vol0.102
s_anti_bump_dis_restr0.096
s_approx_iso_adps0.089
s_similar_adp_cmpnt0.037
s_angle_d0.034
s_bond_d0.017
s_rigid_bond_adp_cmpnt0.006
s_similar_dist
s_from_restr_planes
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1900
Nucleic Acid Atoms
Solvent Atoms417
Heterogen Atoms30

Software

Software
Software NamePurpose
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing