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Crystal structure of the gammadelta T cell costimulatory receptor Junctional Adhesion Molecule-Like Protein, JAML
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other OBTAINED BY MAD PHASING OF A TA6BR12 SOAKED JAML CRYSTAL AND SUBSEQUENT MR INTO THE NATIVE HIGH RESOLUTION DATA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.25 295 3.25 M NA-FORMATE, 0.1 M IMIDAZOLE, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.58 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.946 α = 90 b = 61.946 β = 90 c = 82.477 γ = 90
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 210 KOHZU: DOUBLE CRYSTAL SI(111) 2005-02-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.07812, 0.99984 ALS 8.2.1
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 2.19 50 99.7 0.083 0.083 11.1 3.6 15924 34.9
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) 2.19 2.24 99.2 0.415 0.415 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 MAD THROUGHOUT OBTAINED BY MAD PHASING OF A TA6BR12 SOAKED JAML CRYSTAL AND SUBSEQUENT MR INTO THE NATIVE HIGH RESOLUTION DATA 2.19 50 15098 799 99.3 0.172 0.17 0.1744 0.213 0.2162 RANDOM 37.609
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] 0.16 0.16 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.55 r_dihedral_angle_4_deg 22.573 r_dihedral_angle_3_deg 16.657 r_dihedral_angle_1_deg 8.007 r_scangle_it 4.414 r_scbond_it 2.625 r_angle_refined_deg 1.716 r_mcangle_it 1.642 r_angle_other_deg 1.296 r_mcbond_it 0.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.55 r_dihedral_angle_4_deg 22.573 r_dihedral_angle_3_deg 16.657 r_dihedral_angle_1_deg 8.007 r_scangle_it 4.414 r_scbond_it 2.625 r_angle_refined_deg 1.716 r_mcangle_it 1.642 r_angle_other_deg 1.296 r_mcbond_it 0.862 r_symmetry_vdw_other 0.237 r_nbd_other 0.21 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.199 r_mcbond_other 0.183 r_nbtor_refined 0.17 r_symmetry_vdw_refined 0.141 r_chiral_restr 0.127 r_symmetry_hbond_refined 0.123 r_nbtor_other 0.096 r_metal_ion_refined 0.031 r_bond_refined_d 0.016 r_bond_other_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1828 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 77
Software Software Software Name Purpose SHELX model building RESOLVE model building PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing RESOLVE phasing