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Structure of mCD1d with bound glycolipid BbGL-2c from Borrelia burgdorferi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AKR PDB entry 2AKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 17% polyethylene glycol 3350, 150mM di-ammonium hydrogen citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.706 α = 90 b = 97.791 β = 106.94 c = 55.421 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 ADSC QUANTUM 315r Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing). 2009-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.0 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 2.05 50 93.9 0.042 35.9 4.4 6643 25018
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) 2.05 2.12 90 0.604 3.6 4.4
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 PDB entry 2AKR 2.05 35.07 23963 1023 93.82 0.20952 0.20766 0.2051 0.25102 0.248 RANDOM 53.287
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 -0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.627 r_dihedral_angle_3_deg 15.399 r_dihedral_angle_4_deg 15.189 r_dihedral_angle_1_deg 6.505 r_scangle_it 2.873 r_scbond_it 1.934 r_angle_refined_deg 1.479 r_mcangle_it 1.147 r_mcbond_it 0.618 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.627 r_dihedral_angle_3_deg 15.399 r_dihedral_angle_4_deg 15.189 r_dihedral_angle_1_deg 6.505 r_scangle_it 2.873 r_scbond_it 1.934 r_angle_refined_deg 1.479 r_mcangle_it 1.147 r_mcbond_it 0.618 r_chiral_restr 0.096 r_bond_refined_d 0.012 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 2909 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 109
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling