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Structure of mCD1d with bound glycolipid BbGL-2f from Borrelia burgdorferi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 20% polyethylene glycol 4000, 100mM sodium citrate, 10% n-propanol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.82 56.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.148 α = 90 b = 110.393 β = 90 c = 107.498 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 MARMOSAIC 325 mm CCD Flat collimating mirror, double crystal monochromator, toroid focusing mirror 2007-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.0 SSRL BL9-2
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 1.85 40 91.2 0.061 21.5 3.2 43756 39906 21.2
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) 1 1.85 1.95 94.4 0.383 3.6 3.1 4309
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 2AKR 1.85 39.24 38588 1230 90.92 0.2056 0.20476 0.2231 0.23269 0.2575 RANDOM 25.86
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 33.144 r_dihedral_angle_4_deg 22.899 r_dihedral_angle_3_deg 13.591 r_dihedral_angle_1_deg 6.354 r_scangle_it 3.322 r_scbond_it 2.151 r_angle_refined_deg 1.43 r_mcangle_it 1.295 r_mcbond_it 0.735 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.144 r_dihedral_angle_4_deg 22.899 r_dihedral_angle_3_deg 13.591 r_dihedral_angle_1_deg 6.354 r_scangle_it 3.322 r_scbond_it 2.151 r_angle_refined_deg 1.43 r_mcangle_it 1.295 r_mcbond_it 0.735 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 2941 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 101
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling