8RWB | pdb_00008rwb

Crystal structure of ULBP6 in complex with a blocking antibody

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		proprietary model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	Glycerol 10.0 %v/v MES: 0.10 M pH:6.00 PEG 1K 5.0 %w/v PEG 600 30.0 %w/v

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.551	α = 90
b = 95.803	β = 117.74
c = 97.203	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	PIXEL	DECTRIS EIGER2 S 16M		2022-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9998	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.307	86.031	92.3	0.991	7.2	4		19970

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.307	2.658			0.581

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.307	86.031	19970	1006	52.373	0.219	0.2159	0.2184	0.2865	0.2836	42.239

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]
0.673		0.182	-0.988		0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.953
r_dihedral_angle_3_deg	15.511
r_dihedral_angle_4_deg	13.761
r_dihedral_angle_1_deg	8.385
r_lrange_it	5.15
r_lrange_other	5.149
r_mcangle_it	3.116
r_mcangle_other	3.116
r_scangle_it	2.508
r_scangle_other	2.508
r_mcbond_it	1.769
r_mcbond_other	1.762
r_angle_refined_deg	1.422
r_scbond_it	1.401
r_scbond_other	1.401
r_angle_other_deg	1.069
r_dihedral_angle_other_1_deg	0.776
r_ext_dist_refined_d	0.443
r_nbd_refined	0.151
r_nbd_other	0.151
r_symmetry_nbd_other	0.15
r_nbtor_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.139
r_xyhbond_nbd_refined	0.112
r_symmetry_nbd_refined	0.1
r_symmetry_nbtor_other	0.069
r_chiral_restr	0.046
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4617
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	60

Software

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