3RNK | pdb_00003rnk

Crystal structure of the complex between mouse PD-1 mutant and PD-L2 IgV domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NPU	1NPU,3BOV
experimental model	PDB	3BOV	1NPU,3BOV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	0.1M HEPES pH 7, 0.1M Magnesium chloride, 15% PEG 4000, Vapor diffusion, Sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.75	29.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.057	α = 90
b = 60.246	β = 90
c = 80.087	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315		2008-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.74	50	95.1	0.62	0.63	26.23	5.9	17532	17532

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.74	1.81	69.6		0.155	0.16	4.42	2.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1NPU,3BOV	1.74	48.17	17485	909	94.39	0.1974	0.1947	0.19	0.2469	0.25	RANDOM	25.5806

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]
-1.55			3.2		-1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.647
r_dihedral_angle_4_deg	19.014
r_dihedral_angle_3_deg	14.876
r_dihedral_angle_1_deg	6.661
r_scangle_it	3.878
r_scbond_it	2.317
r_mcangle_it	1.812
r_angle_refined_deg	1.412
r_mcbond_it	0.971
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.647
r_dihedral_angle_4_deg	19.014
r_dihedral_angle_3_deg	14.876
r_dihedral_angle_1_deg	6.661
r_scangle_it	3.878
r_scbond_it	2.317
r_mcangle_it	1.812
r_angle_refined_deg	1.412
r_mcbond_it	0.971
r_chiral_restr	0.102
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1700
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.