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RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH MANGANESE 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 = 130.712 α = 90 b = 130.712 β = 90 c = 251.8 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 3.05 130.712 99.6 0.113 0.125 0.054 11.8 5 79819
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 3.05 3.21 100 0.516 0.516 0.574 0.246 1.5 5.1
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 5THP 3.05 48.01 75867 3888 99.54 0.2197 0.2169 0.2185 0.2735 0.2722 RANDOM 59.586
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] 0.35 0.35 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.784 r_dihedral_angle_3_deg 18.783 r_dihedral_angle_4_deg 17.899 r_dihedral_angle_1_deg 9.488 r_angle_refined_deg 1.434 r_angle_other_deg 1.178 r_chiral_restr 0.049 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 33.784 r_dihedral_angle_3_deg 18.783 r_dihedral_angle_4_deg 17.899 r_dihedral_angle_1_deg 9.488 r_angle_refined_deg 1.434 r_angle_other_deg 1.178 r_chiral_restr 0.049 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 SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing