6S7F
Human CD73 (5'-nucleotidase) in complex with PSB12379 (an AOPCP derivative) in the closed state
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4H2I |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 292.15 | Enter some text here...Crystallization buffer: 5 % (w/v) polyethylene glycol 6000, 0.1 M citric acid pH 5.0-6.0. Crystallization drop:1 uL crystallization buffer + 1 uL of 3 mg/mL protein in 10 mM Tris pH 8.0, 100 uM ZnCl2, 1 mM Inhibitor. Cryobuffer: 25 % (v/v) polyethylene glycol 200, 0.1 MES pH 5.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.91 | α = 90 |
b = 95.66 | β = 90 |
c = 233.22 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | Sagitally bended Si111-crystal | 2013-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.918409 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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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) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
1 | 2.05 | 46.97 | 100 | 0.175 | 0.189 | 0.07 | 0.998 | 8.8 | 7.2 | 38440 | 40.53 |
Highest Resolution Shell | |||||||||||||||||||
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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) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.05 | 2.11 | 100 | 2.576 | 2.769 | 1.003 | 0.272 | 0.8 | 7.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 4h2i | 2.05 | 46.97 | 38386 | 1198 | 99.96 | 0.1814 | 0.1803 | 0.2155 | RANDOM | 64.72 |
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] | |
-7.3593 | -11.2073 | 18.5666 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 13.9 |
t_omega_torsion | 3.83 |
t_angle_deg | 1.15 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4041 |
Nucleic Acid Atoms | |
Solvent Atoms | 205 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
BUSTER | phasing |