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The Crystal Structure of Human CD1b with a Bound Bacterial Glycolipid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GZQ PDB ENTRY 1GZQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 0.1M SODIUM CITRATE PH 5.6, 0.5M AMMONIUM SULFATE, 0.5M LITHIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 3.5 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.974 α = 90 b = 96.974 β = 90 c = 114.834 γ = 120
Symmetry Space Group P 31 2 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 CCD MIRRORS 2002-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 3.1 20 99.9 0.077 34.9 12.8 11697 1
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 3.1 3.21 100 0.604 5.7
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 1GZQ 3.1 19.9 11687 800 100 0.236 0.236 0.2191 0.29 0.278 RANDOM 87
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] 4.68 15.28 4.68 -9.36
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.7 c_mcangle_it 4.2 c_scangle_it 3.91 c_mcbond_it 2.36 c_scbond_it 2.2 c_angle_deg 2 c_improper_angle_d 1.9 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.7 c_mcangle_it 4.2 c_scangle_it 3.91 c_mcbond_it 2.36 c_scbond_it 2.2 c_angle_deg 2 c_improper_angle_d 1.9 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3011 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 74
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling EPMR phasing