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Ligand-induced signalling and conformational change of the 39 kD glycoprotein from human articular chondrocytes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LG2 PDB ENTRY 1LG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE PH 4.6, 25% PEG 4000, 100 MM DTT
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.562 α = 90 b = 122.048 β = 90 c = 136.097 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 113 CCD 2002-09-15 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 1.85 15 99 0.076 9.5 4.4 153614 17.2
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 1.92 98.4 0.519 3.7 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 1LG2 1.85 14.98 153536 728 98.8 0.197 0.197 0.1897 0.225 0.2259 RANDOM 33.2
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] -7.26 -1.25 8.52
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 3.45 c_mcangle_it 2.38 c_scbond_it 2.38 c_mcbond_it 1.65 c_angle_deg 1.6 c_improper_angle_d 1 c_bond_d 0.013 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 3.45 c_mcangle_it 2.38 c_scbond_it 2.38 c_mcbond_it 1.65 c_angle_deg 1.6 c_improper_angle_d 1 c_bond_d 0.013 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 11380 Nucleic Acid Atoms Solvent Atoms 1393 Heterogen Atoms 248
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing FFFEAR phasing CNS refinement