☰ Navigation Tabs
Rhodocetin in complex with the integrin alpha2-A domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GPR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1M Tris pH 8.0,
2.65M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 3.29 62.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.763 α = 90 b = 130.763 β = 90 c = 251.351 γ = 90
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 RAYONIX MX-300 2011-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.006 19.87 99.3 11.9 5.3 83038
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3GPR 3.006 19.867 1.34 82982 4301 99.58 0.2237 0.2206 0.2206 0.27 0.2689 random exclusion
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 11.542 f_angle_d 0.554 f_chiral_restr 0.04 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20622 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 170
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing