3LE7

Crystal structure of PD-L1 from P. dioica in complex with adenine

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.16M sodium acetate trihydrate, 0.1M sodium cacodylate, 24% PEG8000, 3mM Adenine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.81	31.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.323	α = 90
b = 32.159	β = 128.29
c = 112.295	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2009-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.0	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.65	30	92.8	0.09	6.7	4.2	61167	56763

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.65	1.69	85.3		0.07	2	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3h5k	1.65	9.97	48429	41131	2167	84.93	0.214	0.214	0.213	0.249	RANDOM	16.817

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]
0.04		0.05			0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.214
r_dihedral_angle_4_deg	25.509
r_dihedral_angle_3_deg	13.841
r_dihedral_angle_1_deg	6.99
r_scangle_it	3.397
r_angle_refined_deg	2.604
r_scbond_it	2.134
r_mcangle_it	1.633
r_mcbond_it	0.957
r_nbtor_refined	0.383
r_nbd_refined	0.303
r_symmetry_vdw_refined	0.297
r_xyhbond_nbd_refined	0.264
r_symmetry_hbond_refined	0.264
r_chiral_restr	0.117
r_bond_refined_d	0.037
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4100
Nucleic Acid Atoms
Solvent Atoms	659
Heterogen Atoms	62

Software

Software
Software Name	Purpose
HKL-2000	data collection
Il	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Il	phasing