6U6V | pdb_00006u6v

Crystal structure of human PD-1H / VISTA

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6	298	0.3 ul protein in HBS with 0.3 ul of crystallization buffer consisting of 100 mM Bis-Tris:HCl pH 6.0 and 28% (v/v) polyethylene glycol monomethyl ether (MW 2000) (Sigma-Aldrich) under a drop of paraffin oil and silicon oil in a 2:1 ratio

Crystal Properties
Matthews coefficient	Solvent content
1.71	28.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.821	α = 90
b = 55.833	β = 97.69
c = 42.271	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		2016-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9792	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.9	50	95.2	0.097	0.115	0.061	7.4	3.4		10041

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	75.5		0.697	0.844	0.469	0.53		2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	41.89	9503	531	95.24	0.2097	0.2074	0.2141	0.2498	0.2549	RANDOM	38.877

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]
-2.87		-1.19	-0.63		3.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.682
r_dihedral_angle_4_deg	22.203
r_dihedral_angle_3_deg	16.446
r_dihedral_angle_1_deg	7.048
r_angle_refined_deg	1.726
r_angle_other_deg	1.513
r_chiral_restr	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1163
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	14

Software

Software
Software Name	Purpose
HKL-2000	data scaling
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing