☰ Navigation Tabs
Crystal structure of bovine CD1b3 with endogenously bound ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H26 PDB ENTRY 2H26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 100 mM Na cacodylate pH 6.5, 2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.11 60.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.533 α = 90 b = 139.975 β = 90 c = 111.953 γ = 90
Symmetry Space Group P 21 21 2
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 2007-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 50 99.5 0.08 21.5 5 96734 96251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.36 99.8 0.62 2.4 4.9
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 MOLREP THROUGHOUT PDB ENTRY 2H26 2.3 45 96734 90909 4805 99.44 0.20325 0.20093 0.2132 0.24778 0.2595 RANDOM 42.935
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] 0.09 1.08 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.468 r_dihedral_angle_4_deg 22.45 r_dihedral_angle_3_deg 14.666 r_dihedral_angle_1_deg 6.384 r_scangle_it 3.051 r_scbond_it 1.91 r_angle_refined_deg 1.457 r_mcangle_it 1.147 r_mcbond_it 0.591 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.468 r_dihedral_angle_4_deg 22.45 r_dihedral_angle_3_deg 14.666 r_dihedral_angle_1_deg 6.384 r_scangle_it 3.051 r_scbond_it 1.91 r_angle_refined_deg 1.457 r_mcangle_it 1.147 r_mcbond_it 0.591 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 11613 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 583
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling