☰ Navigation Tabs
Structure of mouse CD1d with bound alpha-galactosylsphingamide JG168
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q7Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 295 20% PEG 4000, 8% Tacsimate
Crystal Properties Matthews coefficient Solvent content 2.81 56.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.203 α = 90 b = 107.466 β = 90 c = 109.55 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 CCD ADSC QUANTUM 315r 2015-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.15 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.75 40 99.7 0.061 0.069 0.033 14.3 4.3 51068
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 100 0.509 0.834 4.3
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 2Q7Y 1.75 30.2 49952 1050 99.72 0.2032 0.20283 0.2112 0.22134 0.2273 RANDOM 32.776
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.307 r_dihedral_angle_4_deg 19.723 r_dihedral_angle_3_deg 11.424 r_dihedral_angle_1_deg 6.035 r_long_range_B_refined 5.485 r_long_range_B_other 5.255 r_scangle_other 3.265 r_mcangle_other 2.944 r_mcangle_it 2.943 r_scbond_it 1.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.307 r_dihedral_angle_4_deg 19.723 r_dihedral_angle_3_deg 11.424 r_dihedral_angle_1_deg 6.035 r_long_range_B_refined 5.485 r_long_range_B_other 5.255 r_scangle_other 3.265 r_mcangle_other 2.944 r_mcangle_it 2.943 r_scbond_it 1.968 r_scbond_other 1.965 r_mcbond_it 1.743 r_mcbond_other 1.728 r_angle_refined_deg 1.329 r_angle_other_deg 0.976 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2930 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction HKL data reduction