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CD1b in complex with GM2 ganglioside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.1 293 20 DEGREE C 2UL OF PROTEIN + 1UL OF MOTHER LIQUOR 0.2M LITHIUM NITRATE 20% W/V POLYETHYLENE GLYCOL 3350, PH 7.1
Crystal Properties Matthews coefficient Solvent content 3.24 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.527 α = 90 b = 176.885 β = 90 c = 75.25 γ = 90
Symmetry Space Group C 2 2 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 ADSC CCD 2001-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.8 100 87.4 0.103 13.7 6.8 89500 -0.5 95.2
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 2.8 2.9 71.1 0.325 1.8
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 1CD1 2.8 34.78 12918 535 87.4 0.225 0.225 0.2149 0.273 0.2643 RANDOM 50.2
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] 2.43 -6.93 4.5
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.5 c_scangle_it 5.72 c_scbond_it 4.01 c_mcangle_it 3.9 c_mcbond_it 2.35 c_angle_deg 1.6 c_improper_angle_d 1.46 c_bond_d 0.012 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.5 c_scangle_it 5.72 c_scbond_it 4.01 c_mcangle_it 3.9 c_mcbond_it 2.35 c_angle_deg 1.6 c_improper_angle_d 1.46 c_bond_d 0.012 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 2992 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 86
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing