8TBB | pdb_00008tbb

F9S, novel TIM-3 targeting antibody, bound to IgV domain of TIM-3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OYP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystals for the TIM-3-F9S Fab complex were obtained in a condition made up of a combination of 0.1M BICINE, pH 9.0 and 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.805	α = 90
b = 57.005	β = 106
c = 80.453	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	PIXEL	DECTRIS PILATUS 6M	Si (111) double crystal	2017-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.987	SSRL	BL14-1

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	2.4	35	99.8	0.97	11.2	3.9		23828

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	2.4	2.8	99.9		0.88		3.3

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	THROUGHOUT	2.5	35	22188	1117	99.905	0.194	0.1909	0.2	0.2412	0.25	31.428

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]
4.523		-0.607	-2.429		-1.499

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.972
r_dihedral_angle_2_deg	16.287
r_dihedral_angle_6_deg	16.138
r_dihedral_angle_1_deg	10.58
r_lrange_other	9.241
r_lrange_it	9.233
r_scangle_it	7.316
r_scangle_other	7.315
r_mcangle_it	5.495
r_mcangle_other	5.494
r_scbond_it	5.124
r_scbond_other	5.123
r_mcbond_it	3.801
r_mcbond_other	3.794
r_angle_refined_deg	0.375
r_xyhbond_nbd_refined	0.255
r_symmetry_nbd_other	0.243
r_nbd_other	0.241
r_nbd_refined	0.227
r_nbtor_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.173
r_angle_other_deg	0.139
r_symmetry_nbd_refined	0.128
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.02
r_symmetry_xyhbond_nbd_other	0.005
r_bond_refined_d	0.001
r_gen_planes_refined	0.001
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4145
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing