2OYP

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EAJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52911.8 M Ammonium Sulfate, 0.1 M Sodium Citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.8734.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 23α = 90
b = 52.809β = 100.94
c = 38.941γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.4503NSLSX29A

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.953096.20.0730.081123.664576457
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)RedundancyNumber Unique Reflections (All)
11.952.0272.60.1360.1416.82.9470

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1eaj1.952306442644230596.090.1580.1580.1560.2RANDOM20.153
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]
-0.980.38-0.942.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.719
r_dihedral_angle_4_deg23.543
r_dihedral_angle_3_deg15.006
r_dihedral_angle_1_deg6.154
r_scangle_it3.038
r_scbond_it1.797
r_angle_refined_deg1.195
r_mcangle_it1.159
r_mcbond_it0.638
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.719
r_dihedral_angle_4_deg23.543
r_dihedral_angle_3_deg15.006
r_dihedral_angle_1_deg6.154
r_scangle_it3.038
r_scbond_it1.797
r_angle_refined_deg1.195
r_mcangle_it1.159
r_mcbond_it0.638
r_nbtor_refined0.303
r_nbd_refined0.193
r_symmetry_vdw_refined0.184
r_symmetry_hbond_refined0.149
r_xyhbond_nbd_refined0.139
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms866
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms5

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing