☰ Navigation Tabs
Structure of a highly potent short-chain galactosyl ceramide agonist bound to CD1D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CD1 PDB Entry 1CD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 277 PEG 4000, calcium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.451 α = 90 b = 77.045 β = 107.63 c = 111.014 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 120 CCD ADSC QUANTUM 315 2004-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9537 ALS 8.2.2
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 2.2 50 0.075 20.8 2.4 48471
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 2.2 2.25 86.9 0.37 2
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 1CD1 2.2 39.68 44014 44014 1414 93.72 0.24321 0.24156 0.2407 0.29368 0.2896 RANDOM 71.352
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] -0.01 0.02 -0.04 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.895 r_dihedral_angle_4_deg 22.531 r_dihedral_angle_3_deg 17.989 r_dihedral_angle_1_deg 5.792 r_scangle_it 2.552 r_angle_refined_deg 1.848 r_scbond_it 1.757 r_mcangle_it 1.135 r_mcbond_it 0.737 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.895 r_dihedral_angle_4_deg 22.531 r_dihedral_angle_3_deg 17.989 r_dihedral_angle_1_deg 5.792 r_scangle_it 2.552 r_angle_refined_deg 1.848 r_scbond_it 1.757 r_mcangle_it 1.135 r_mcbond_it 0.737 r_nbtor_refined 0.313 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.149 r_bond_refined_d 0.015 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 5911 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 214
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction CCP4 data scaling MOLREP phasing