2Y62

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.521% 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 = 97.76α = 90
b = 52.46β = 118.08
c = 58.25γ = 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
11.0810990.0916.26.1110340
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)
11.081.197.70.423.64

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 1N551.08101047035510990.10890.1328RANDOM
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
1941.592293.29
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.092
s_zero_chiral_vol0.091
s_approx_iso_adps0.077
s_anti_bump_dis_restr0.074
s_similar_adp_cmpnt0.034
s_angle_d0.032
s_bond_d0.015
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
s_from_restr_planes
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1900
Nucleic Acid Atoms
Solvent Atoms484
Heterogen Atoms30

Software

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