7DV4 | pdb_00007dv4

Crystal structure of anti-CTLA-4 VH domain in complex with human CTLA-4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OSK	3OSK,5AZE
experimental model	PDB	5AZE	3OSK,5AZE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	100 mM sodium citrate, 10% (w/v) PEG 6000, pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.591	α = 90
b = 110.336	β = 90
c = 134.185	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	PIXEL	DECTRIS EIGER X 16M		2019-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979183	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.38	44.73	99.8	0.037	0.041	0.016	0.999	23.5	6.4		45646

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	2.38	2.46	100		0.867	0.953	0.391	0.693		5.7

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	3OSK,5AZE	2.38	42.33	43328	2247	99.66	0.223	0.2212	0.2232	0.258	0.2566	RANDOM

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]
1.34			1.31		-2.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.097
r_dihedral_angle_3_deg	14.078
r_dihedral_angle_4_deg	13.328
r_dihedral_angle_1_deg	6.228
r_angle_other_deg	1.421
r_angle_refined_deg	1.226
r_chiral_restr	0.049
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7014
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	8

Software

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