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RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH YTTRIUM BOUND
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5THP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1 M TRIS, 2.65 M AMMONIUM SULPHATE
Crystal Properties Matthews coefficient Solvent content 3.52 65.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.846 α = 90 b = 130.846 β = 90 c = 251.167 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 IMAGE PLATE RIGAKU mirrors 2010-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 3.15 130.846 100 0.163 0.173 0.056 13.5 9.4 72738
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.32 100 0.732 0.732 0.774 0.25 1 9.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5THP 3.15 46.94 69049 3621 99.95 0.2177 0.2149 0.2712 0.2685 RANDOM 60.833
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] 0.06 0.06 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.088 r_dihedral_angle_3_deg 18.636 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_1_deg 9.491 r_angle_refined_deg 1.423 r_angle_other_deg 1.173 r_chiral_restr 0.048 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.088 r_dihedral_angle_3_deg 18.636 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_1_deg 9.491 r_angle_refined_deg 1.423 r_angle_other_deg 1.173 r_chiral_restr 0.048 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21486 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing