8S6Z | pdb_00008s6z

CD28 in complex with the antibody Fab fragment AI3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6UTA
experimental model	PDB	6O8D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	Crystallization trials were set up using the CD28-AI3 Fab at 15.8 mg/mL in phosphate buffered saline (PBS) pH 7.4. Drops were set up using 100 nl protein and 100 nL reservoir solution containing 200 mM zinc acetate, 0.1 M imidazole pH 8.0, 20% w/v PEG 3000.

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.874	α = 90
b = 117.939	β = 90
c = 145.719	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		2023-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.999873	MAX IV	BioMAX

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	3.05	91.843	100	0.243	0.268	0.112	0.995	8.2	10.3		25981

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	3.05	3.26			1.912	2.112	0.884	0.602		10.5

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	3.05	91.843	25926	1327	99.969	0.201	0.1975	0.1974	0.2575	0.255	91.441

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]
7.175			-5.263		-1.912

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.976
r_lrange_other	15.785
r_lrange_it	15.784
r_dihedral_angle_6_deg	14.974
r_scangle_it	12.172
r_scangle_other	12.171
r_mcangle_it	10.17
r_mcangle_other	10.169
r_scbond_it	8.117
r_scbond_other	8.116
r_mcbond_it	6.864
r_mcbond_other	6.863
r_dihedral_angle_1_deg	5.844
r_dihedral_angle_2_deg	4.267
r_angle_refined_deg	1.687
r_angle_other_deg	0.586
r_nbd_other	0.256
r_symmetry_xyhbond_nbd_refined	0.248
r_symmetry_nbd_refined	0.218
r_symmetry_nbd_other	0.2
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.177
r_metal_ion_refined	0.137
r_ncsr_local_group_3	0.113
r_symmetry_metal_ion_refined	0.109
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.078
r_symmetry_xyhbond_nbd_other	0.071
r_ncsr_local_group_1	0.057
r_ncsr_local_group_2	0.051
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8507
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	251

Software

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