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Structure of mouse CD1d in complex with C10Ph
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GML PDB entry 3GML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 295 0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.44 49.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.67 α = 90 b = 97.87 β = 106.44 c = 55.41 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 MARMOSAIC 325 mm CCD flat mirror 2007-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9795 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 30 98.2 0.031 21 3.8 46034 46034 -3 34.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 97.7 0.481 2.6 3.8 7207
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 PDB entry 3GML 1.7 27.8 46033 43699 2334 98.32 0.17864 0.17864 0.1766 0.1836 0.21767 0.228 RANDOM 27.145
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] -1.75 -1.5 2.05 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.4 r_dihedral_angle_4_deg 20.876 r_dihedral_angle_3_deg 14.539 r_dihedral_angle_1_deg 6.644 r_scangle_it 5.04 r_scbond_it 3.333 r_mcangle_it 2.224 r_angle_refined_deg 2.114 r_mcbond_it 1.37 r_chiral_restr 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.4 r_dihedral_angle_4_deg 20.876 r_dihedral_angle_3_deg 14.539 r_dihedral_angle_1_deg 6.644 r_scangle_it 5.04 r_scbond_it 3.333 r_mcangle_it 2.224 r_angle_refined_deg 2.114 r_mcbond_it 1.37 r_chiral_restr 0.151 r_bond_refined_d 0.023 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2975 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 230
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling