7PBB

Crystal structure of CD73 in complex with caffeine in the open form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H2G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2927 mg/mL protein concentration, 100 mM Tris pH 7.8, 10 % PEG6000, equal amounts of protein and reservoir. Following crystal formation (1-2 days), the crystals were transferred to soaking solution containing reservoir solution and 50 mM caffeine. Crystals were then transferred to cryo solution containing an additional 20 % glycerol, soaked for ~2-5 min, and flash frozen in liquid nitrogen.
Crystal Properties
Matthews coefficientSolvent content
2.4349.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.243α = 90
b = 131.799β = 90
c = 66.316γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
11.4747.26990.1720.1870.0720.9957.66.699458
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)
11.471.595.41.4431.5660.5970.3486.5

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 SYNTHESISTHROUGHOUT4h2g1.4747.2694572482098.880.17380.17260.1956RANDOM13.828
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]
0.090.2-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.752
r_dihedral_angle_4_deg20.103
r_dihedral_angle_3_deg12.726
r_dihedral_angle_1_deg9.208
r_angle_refined_deg1.966
r_angle_other_deg1.57
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.013
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.752
r_dihedral_angle_4_deg20.103
r_dihedral_angle_3_deg12.726
r_dihedral_angle_1_deg9.208
r_angle_refined_deg1.966
r_angle_other_deg1.57
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.013
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4062
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing