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Crystal Structure of the Human TSG-6 Link Module
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UUH 1UUH - crystal structure of CD44
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 A 2.5 ul drop formed from equal amounts of protein solution (7 mg/ml solution in approximately 25mM TrisHCl and 75mM NaCl) and well solution was equilibrated against 1 ml well solution (2 M Ammonium Sulphate, 2 % v/v PEG 400 and 0.1M Sodium Hepes (pH 7.5)), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.12 70.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.816 α = 90 b = 75.87 β = 103.42 c = 90.674 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 4 2005-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 88.04 99.14 0.071 6.35 4.08 69439
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 98.62 0.41 1.51 3.98
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 1UUH - crystal structure of CD44 1.9 88.04 65938 3499 98.96 0.19596 0.19439 0.2245 0.22588 0.253 RANDOM 21.78
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] -0.19 0.66 0.3 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.67 r_dihedral_angle_4_deg 17.585 r_dihedral_angle_1_deg 14.882 r_dihedral_angle_3_deg 14.615 r_scangle_it 2.874 r_scbond_it 2.086 r_angle_refined_deg 1.66 r_mcangle_it 1.273 r_mcbond_it 0.874 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.67 r_dihedral_angle_4_deg 17.585 r_dihedral_angle_1_deg 14.882 r_dihedral_angle_3_deg 14.615 r_scangle_it 2.874 r_scbond_it 2.086 r_angle_refined_deg 1.66 r_mcangle_it 1.273 r_mcbond_it 0.874 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.241 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.118 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3743 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 191
Software Software Software Name Purpose DNA data collection DM model building REFMAC refinement MOSFLM data reduction SCALA data scaling DM phasing