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Crystal Structure of the Thrombospondin-1 N-terminal Domain at 1.45A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z78 PDB ENTRY 1Z78
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 300 30% PEG1500 and 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.2 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.31 α = 90 b = 40.489 β = 106.99 c = 60.086 γ = 90
Symmetry Space Group P 1 21 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 315 2005-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.00931 APS 19-ID
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 1.45 30 95.8 0.068 39.7 3.8 34155 34155 29.2
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) 1.45 1.5 68.7 0.376 2.5 2.3 2422
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1Z78 1.45 22.86 30931 30931 2575 94.38 0.1863 0.18559 0.18301 0.1847 0.21672 0.1847 RANDOM 25.962
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.762 r_dihedral_angle_4_deg 19.138 r_dihedral_angle_3_deg 13.208 r_dihedral_angle_1_deg 6.165 r_rigid_bond_restr 5.607 r_scbond_it 5.434 r_scangle_it 5.186 r_sphericity_free 4.395 r_sphericity_bonded 3.841 r_mcangle_it 2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.762 r_dihedral_angle_4_deg 19.138 r_dihedral_angle_3_deg 13.208 r_dihedral_angle_1_deg 6.165 r_rigid_bond_restr 5.607 r_scbond_it 5.434 r_scangle_it 5.186 r_sphericity_free 4.395 r_sphericity_bonded 3.841 r_mcangle_it 2.27 r_mcbond_it 1.473 r_angle_refined_deg 1.467 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1609 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing