3ILQ

Structure of mCD1d with bound glycolipid BbGL-2c from Borrelia burgdorferi


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AKRPDB entry 2AKR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529517% polyethylene glycol 3350, 150mM di-ammonium hydrogen citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4449.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.706α = 90
b = 97.791β = 106.94
c = 55.421γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rVertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).2009-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.0SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.055093.90.04235.94.4664325018
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.052.12900.6043.64.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2AKR2.0535.0723963102393.820.209520.207660.25102RANDOM53.287
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]
0.010.01-0.030.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.627
r_dihedral_angle_3_deg15.399
r_dihedral_angle_4_deg15.189
r_dihedral_angle_1_deg6.505
r_scangle_it2.873
r_scbond_it1.934
r_angle_refined_deg1.479
r_mcangle_it1.147
r_mcbond_it0.618
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.627
r_dihedral_angle_3_deg15.399
r_dihedral_angle_4_deg15.189
r_dihedral_angle_1_deg6.505
r_scangle_it2.873
r_scbond_it1.934
r_angle_refined_deg1.479
r_mcangle_it1.147
r_mcbond_it0.618
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.007
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 AtomsNumber
Protein Atoms2909
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms109

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling