6Y8K

Crystal structure of CD137 in complex with the cyclic peptide BCY10916


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6MI2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.6293.151.5 M lithium sulfate monohydrate, 0.1M sodium acetate trihydrate, pH 4.6
Crystal Properties
Matthews coefficientSolvent content
3.9268.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.47α = 90
b = 122.47β = 90
c = 122.47γ = 90
Symmetry
Space GroupP 42 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
12.0140.8571000.0420.043145.739.121496
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)
12.012.052.2162.2440.756

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6MI22.01140.85721467107099.8510.2850.28310.31463.013
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg39.94
r_dihedral_angle_2_deg28.803
r_dihedral_angle_3_deg17.881
r_lrange_other12.366
r_lrange_it12.36
r_dihedral_angle_4_deg11.678
r_scangle_it9.773
r_scangle_other9.767
r_mcangle_it8.164
r_mcangle_other8.158
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg39.94
r_dihedral_angle_2_deg28.803
r_dihedral_angle_3_deg17.881
r_lrange_other12.366
r_lrange_it12.36
r_dihedral_angle_4_deg11.678
r_scangle_it9.773
r_scangle_other9.767
r_mcangle_it8.164
r_mcangle_other8.158
r_dihedral_angle_1_deg8.054
r_scbond_it7.12
r_scbond_other7.113
r_mcbond_it6.076
r_mcbond_other6.07
r_angle_other_deg2.464
r_angle_refined_deg1.798
r_nbd_other0.278
r_symmetry_nbd_other0.234
r_nbd_refined0.231
r_symmetry_nbd_refined0.204
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.159
r_symmetry_xyhbond_nbd_refined0.15
r_symmetry_nbtor_other0.087
r_chiral_restr0.076
r_symmetry_xyhbond_nbd_other0.043
r_bond_other_d0.037
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1072
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing