2OYP | pdb_00002oyp

T Cell Immunoglobulin Mucin-3 Crystal Structure Revealed a Galectin-9-independent Binding Surface

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EAJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	1.8 M Ammonium Sulfate, 0.1 M Sodium Citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 23	α = 90
b = 52.809	β = 100.94
c = 38.941	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	CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.4503	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.95	30	96.2	0.073	0.081	12	3.6	6457	6457

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02	72.6		0.136	0.141	6.8	2.9	470

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1eaj	1.952	30	6442	6442	305	96.09	0.158	0.158	0.156	0.16	0.2	0.2	RANDOM	20.153

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]
-0.98		0.38	-0.94		2.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.719
r_dihedral_angle_4_deg	23.543
r_dihedral_angle_3_deg	15.006
r_dihedral_angle_1_deg	6.154
r_scangle_it	3.038
r_scbond_it	1.797
r_angle_refined_deg	1.195
r_mcangle_it	1.159
r_mcbond_it	0.638
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.719
r_dihedral_angle_4_deg	23.543
r_dihedral_angle_3_deg	15.006
r_dihedral_angle_1_deg	6.154
r_scangle_it	3.038
r_scbond_it	1.797
r_angle_refined_deg	1.195
r_mcangle_it	1.159
r_mcbond_it	0.638
r_nbtor_refined	0.303
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.184
r_symmetry_hbond_refined	0.149
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	866
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.