6Y8K

Crystal structure of CD137 in complex with the cyclic peptide BCY10916

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MI2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	293.15	1.5 M lithium sulfate monohydrate, 0.1M sodium acetate trihydrate, pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.47	α = 90
b = 122.47	β = 90
c = 122.47	γ = 90

Symmetry
Space Group	P 42 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2019-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.01	40.857	100	0.042	0.043	1	45.7	39.1		21496

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)	Redundancy	Number Unique Reflections (All)
1	2.01	2.05			2.216	2.244	0.756

Refinement

Statistics
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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6MI2	2.011	40.857	21467	1070	99.851	0.285	0.2831	0.314	63.013

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
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	39.94
r_dihedral_angle_2_deg	28.803
r_dihedral_angle_3_deg	17.881
r_lrange_other	12.366
r_lrange_it	12.36
r_dihedral_angle_4_deg	11.678
r_scangle_it	9.773
r_scangle_other	9.767
r_mcangle_it	8.164
r_mcangle_other	8.158
r_dihedral_angle_1_deg	8.054
r_scbond_it	7.12
r_scbond_other	7.113
r_mcbond_it	6.076
r_mcbond_other	6.07
r_angle_other_deg	2.464
r_angle_refined_deg	1.798
r_nbd_other	0.278
r_symmetry_nbd_other	0.234
r_nbd_refined	0.231
r_symmetry_nbd_refined	0.204
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.15
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.076
r_symmetry_xyhbond_nbd_other	0.043
r_bond_other_d	0.037
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1072
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing