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Crystal structure of mouse CD1d in complex with ganglioside GD3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GAZ PDB code 2GAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 22% PEG 4000, 10% isopropanol, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.656 α = 90 b = 98.447 β = 106.68 c = 55.486 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 2010-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 50 99 14675 14675 1 1
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 MOLECULAR REPLACEMENT THROUGHOUT PDB code 2GAZ 2.5 49.21 13931 738 98.4 0.19663 0.19446 0.2273 0.23815 0.2705 RANDOM 54.644
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] -0.64 0.06 0.62 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.46 r_dihedral_angle_4_deg 14.775 r_dihedral_angle_3_deg 13.75 r_dihedral_angle_1_deg 5.62 r_scangle_it 1.805 r_angle_refined_deg 1.576 r_scbond_it 1.112 r_mcangle_it 0.682 r_mcbond_it 0.345 r_chiral_restr 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.46 r_dihedral_angle_4_deg 14.775 r_dihedral_angle_3_deg 13.75 r_dihedral_angle_1_deg 5.62 r_scangle_it 1.805 r_angle_refined_deg 1.576 r_scbond_it 1.112 r_mcangle_it 0.682 r_mcbond_it 0.345 r_chiral_restr 0.178 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2911 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 209
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling