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Crystal structure of a collagen II fragment containing the binding site of PEDF and COMP, (POG)4-LKG HRG FTG LQG-POG(4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 298 1.5 M Ammonium sulphate and 0.1 M BIS-TRIS propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.98 37.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.97 α = 90 b = 23.64 β = 92.702 c = 107.939 γ = 90
Symmetry Space Group I 1 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 PIXEL DECTRIS PILATUS 2M-F 2012-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.80000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 0.98 31.02 99.6 0.06 0.065 0.065 0.999 11.9 5.8 47365 9.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.98 0.99 98.7 0.812 0.899 0.541 0.949 2.2 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4axy 1 31.02 1.35 43777 2211 99.49 0.1536 0.1519 0.1525 0.1866 0.1878 15.78
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.2554 f_angle_d 1.5355 f_chiral_restr 0.0677 f_bond_d 0.0154 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 732 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing