3BP5 | pdb_00003bp5

Crystal structure of the mouse PD-1 and PD-L2 complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NPU	1npu, 1pkq
experimental model	PDB	1PKQ	1npu, 1pkq

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Sitting drop	8.5	291	20% PEG 6000, 0.1 M Tris pH 8.5, Sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.933	α = 90
b = 84.056	β = 107.88
c = 52.108	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315		2007-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9792	NSLS	X29A

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	1.7	30	99.2	0.078	9.8	4.6		39403

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	1.7	1.76	97.8		0.573		3.5

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 (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, 1pkq	1.8	24.95	39378	31433	1666	98.62	0.19169	0.1897	0.19	0.22848	0.23	RANDOM	29.223

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]
-0.28		0.34	1.34		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.161
r_dihedral_angle_4_deg	20.965
r_dihedral_angle_3_deg	15.806
r_dihedral_angle_1_deg	11.976
r_scangle_it	4.652
r_mcangle_it	4.287
r_scbond_it	3.234
r_mcbond_it	2.987
r_angle_refined_deg	1.347
r_nbtor_refined	0.309
r_nbd_refined	0.183
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.162
r_symmetry_hbond_refined	0.13
r_chiral_restr	0.098
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2406
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	6

Software

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