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The Crystal Structure of Tumor Endothelial Marker 8 (TEM8) extracellular domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.1M sodium citrate trihydrate (pH 5.6), 0.2M ammonium acetate, 20% (w/v) polyethylene glycol 4000, 0.1M hexammine cobalt (III) chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.91 35.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.895 α = 63.68 b = 66.106 β = 88.19 c = 74.439 γ = 59.94
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 2008-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 64.68 86821
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 1SHU 1.8 50 86821 4573 87.9 0.19434 0.19249 0.1903 0.22927 0.1955 RANDOM 16.504
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] -0.61 -0.11 0.43 0.09 -0.83 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.371 r_dihedral_angle_3_deg 14.008 r_dihedral_angle_4_deg 13.645 r_dihedral_angle_1_deg 4.982 r_scangle_it 1.849 r_scbond_it 1.049 r_angle_refined_deg 0.887 r_mcangle_it 0.625 r_mcbond_it 0.308 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.371 r_dihedral_angle_3_deg 14.008 r_dihedral_angle_4_deg 13.645 r_dihedral_angle_1_deg 4.982 r_scangle_it 1.849 r_scbond_it 1.049 r_angle_refined_deg 0.887 r_mcangle_it 0.625 r_mcbond_it 0.308 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 9012 Nucleic Acid Atoms Solvent Atoms 1353 Heterogen Atoms 78
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling