6TW0

Human CD73 (ecto 5'-nucleotidase) in complex with PSB12690 (an AOPCP derivative, compound 10 in publication) in the closed state


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291Reservoir: 5 % (w/v) polyethylene glycol 6000, 0.1 M NaMES pH 5.5. Drop: 1 microL crystallization buffer + 1 microL of 3 mg/mL protein in 10 mM Tris pH 8.0, 100 microM ZnCl2 and 1 mM of compound. Cryo buffer: 25% PEG200, 0.1 M NaMES pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.6453.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.451α = 90
b = 98.343β = 90
c = 233.75γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-06-18MSINGLE 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)Rpim 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
12.548.1299.70.3490.3750.1370.9925.27.32222666.87
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.699.65.0075.4022.0070.1797.1

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 SYNTHESISTHROUGHOUT4h2i2.548.122217859399.680.23690.23610.2656RANDOM96.91
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]
17.2808-42.43725.1562
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion16.38
t_omega_torsion3.9
t_angle_deg1.12
t_bond_d0.008
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_torsion16.38
t_omega_torsion3.9
t_angle_deg1.12
t_bond_d0.008
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_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4040
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms44

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
BUSTERphasing