8TFT | pdb_00008tft

Fab of O13-1 human IgG1 antibody bound to IgV domain of human TIM-3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FQQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.1 MIB buffer (Sodium malonate dibasic monohydrate, Imidazole, Boric acid), pH 6.0 and 25% w/v PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 218.338	α = 90
b = 69.785	β = 99.897
c = 93.632	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 PILATUS 6M		2017-01-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.97	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	38.9	98.3	0.065	0.93	9.1	3.5		69615

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	2.2	2.5			0.66

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	2.3	37.003	60928	1218	98.228	0.245	0.2443	0.25	0.2711	0.27	60.959

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		-4.112	0.539		1.479

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.095
r_dihedral_angle_6_deg	14.052
r_lrange_it	8.443
r_lrange_other	8.443
r_dihedral_angle_1_deg	7.25
r_dihedral_angle_2_deg	5.876
r_mcangle_it	5.829
r_mcangle_other	5.828
r_scangle_it	5.119
r_scangle_other	5.119
r_mcbond_it	3.573
r_mcbond_other	3.573
r_scbond_it	3.049
r_scbond_other	3.049
r_angle_refined_deg	0.964
r_symmetry_xyhbond_nbd_refined	0.374
r_angle_other_deg	0.335
r_xyhbond_nbd_refined	0.309
r_nbd_refined	0.206
r_symmetry_nbd_other	0.192
r_symmetry_nbd_refined	0.181
r_nbtor_refined	0.176
r_nbd_other	0.148
r_ncsr_local_group_3	0.117
r_ncsr_local_group_2	0.096
r_ncsr_local_group_1	0.093
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.042
r_symmetry_xyhbond_nbd_other	0.014
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8259
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	28

Software

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