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Structure of mouse CD1d in complex with dioleoyl-phosphatidic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q7Y PDB entry 2Q7Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20% PEG 4000, 0.2M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.72 54.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.2 α = 90 b = 106.3 β = 90 c = 107.48 γ = 90
Symmetry Space Group P 21 21 21
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 PSI PILATUS 6M 2013-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.24 75.58 99.7 0.123 10.6 5.3 23912 23843 29.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.24 2.37 99.3 0.552 3.1 5.5 3414
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 (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 PDB entry 2Q7Y 2.24 75.58 22578 22578 1221 99.57 0.2167 0.21476 0.2139 0.25153 0.2502 RANDOM 27.478
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] 0.06 -0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.84 r_dihedral_angle_4_deg 27.215 r_dihedral_angle_3_deg 16.524 r_dihedral_angle_1_deg 6.32 r_angle_refined_deg 1.421 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.84 r_dihedral_angle_4_deg 27.215 r_dihedral_angle_3_deg 16.524 r_dihedral_angle_1_deg 6.32 r_angle_refined_deg 1.421 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2964 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 104
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling