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RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND ZINC
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 = 131.399 α = 90 b = 131.399 β = 90 c = 251.358 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 2.9 131.399 98.6 0.089 0.095 0.034 18.4 7.8 92641
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 2.9 3.06 97.6 0.552 0.552 0.59 0.21 1.4 7.8
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 2.9 47 88062 4534 98.53 0.2311 0.2282 0.2297 0.2849 0.2842 RANDOM 55.617
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] 1.09 1.09 -2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.665 r_dihedral_angle_3_deg 18.46 r_dihedral_angle_4_deg 18.282 r_dihedral_angle_1_deg 9.271 r_angle_refined_deg 1.37 r_angle_other_deg 1.166 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.665 r_dihedral_angle_3_deg 18.46 r_dihedral_angle_4_deg 18.282 r_dihedral_angle_1_deg 9.271 r_angle_refined_deg 1.37 r_angle_other_deg 1.166 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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