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RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH PRASEDYMIUM
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 = 132.351 α = 90 b = 132.351 β = 90 c = 254.244 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 3.5 132.351 99.9 0.141 0.154 0.06 9.4 6.8 54903
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 3.5 3.69 99.5 0.478 0.478 0.528 0.22 1.4 6.3
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 FOURIER SYNTHESIS THROUGHOUT 5THP 3.5 48.57 50794 2746 97.47 0.2941 0.29 0.2957 0.3686 0.3691 RANDOM 116.26
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] 0.17 0.17 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.264 r_dihedral_angle_4_deg 18.742 r_dihedral_angle_3_deg 18.336 r_dihedral_angle_1_deg 9.414 r_angle_refined_deg 1.451 r_angle_other_deg 1.121 r_chiral_restr 0.046 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.264 r_dihedral_angle_4_deg 18.742 r_dihedral_angle_3_deg 18.336 r_dihedral_angle_1_deg 9.414 r_angle_refined_deg 1.451 r_angle_other_deg 1.121 r_chiral_restr 0.046 r_bond_refined_d 0.005 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