6XUQ

Human Ecto-5'-nucleotidase (CD73) in complex with A1618 (compound 1b in publication) in the closed state in crystal form III


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H2I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8291Reservoir: 7.5 % PEG 6.000, 0.1 M MES pH 6.2. Drop: 1 micro-L crystallization buffer + 1 micro-L of 3 mg/mL CD73 in 10 mM Tris pH 8.0, 10 micro-M ZnCl2 and 1 mM of compound. Cryo: 20% PEG200 in crystallization drop
Crystal Properties
Matthews coefficientSolvent content
2.3848.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.09α = 90
b = 93.85β = 90
c = 235.66γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.9747.1399.60.120.1420.9986.813.4828020253.22
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.972.0999.23.3813.9840.1350.373.528

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4h2i1.9746.2142108110399.80.2130.2120.239RANDOM67.82
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]
-1.9834-0.65472.6381
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.48
t_omega_torsion3.49
t_angle_deg1.19
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.48
t_omega_torsion3.49
t_angle_deg1.19
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3997
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms40

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PDB_EXTRACTdata extraction
BUSTERphasing