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Structure of mouse CD1d in complex with PBS-25
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 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.71 α = 90 b = 97.73 β = 106.52 c = 55.49 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 2008-04-14 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 99.5 0.031 23.3 4.1 46664 46664 -3 31.9
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 98.8 0.336 4 3.9 7300
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3GML 1.7 27.78 46663 44302 2361 99.59 0.17784 0.17784 0.17585 0.21569 0.2341 RANDOM 23.566
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] -1.5 -1.45 1.48 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.153 r_dihedral_angle_4_deg 21.15 r_dihedral_angle_3_deg 13.977 r_dihedral_angle_1_deg 6.522 r_scangle_it 5.077 r_scbond_it 3.327 r_mcangle_it 2.177 r_angle_refined_deg 2.099 r_mcbond_it 1.314 r_chiral_restr 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.153 r_dihedral_angle_4_deg 21.15 r_dihedral_angle_3_deg 13.977 r_dihedral_angle_1_deg 6.522 r_scangle_it 5.077 r_scbond_it 3.327 r_mcangle_it 2.177 r_angle_refined_deg 2.099 r_mcbond_it 1.314 r_chiral_restr 0.153 r_bond_refined_d 0.022 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2975 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 222
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling