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Crystal Structure of Thrombospondin-1 N-terminal Domain in P1 Form at 1.85A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z78 PDB code: 1Z78
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 30% PEG1500 and 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.03 39.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.024 α = 73.63 b = 41.709 β = 89.59 c = 59.986 γ = 75.73
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 2004-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.07812 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 1.85 30 94 0.051 21.08 2.4 29466 29466 30.6
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) 1.85 1.95 75.4 0.24 2.91 2.1 2388
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 code: 1Z78 1.85 24.43 27640 27640 1471 94.72 0.1899 0.18996 0.18668 0.1904 0.2498 0.1857 RANDOM 23.688
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] 0.02 -0.11 -0.01 0.11 0.03 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.155 r_dihedral_angle_4_deg 24.787 r_dihedral_angle_3_deg 17.042 r_dihedral_angle_1_deg 7.997 r_scangle_it 5.207 r_scbond_it 3.256 r_mcangle_it 2.008 r_angle_refined_deg 1.814 r_mcbond_it 1.269 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.155 r_dihedral_angle_4_deg 24.787 r_dihedral_angle_3_deg 17.042 r_dihedral_angle_1_deg 7.997 r_scangle_it 5.207 r_scbond_it 3.256 r_mcangle_it 2.008 r_angle_refined_deg 1.814 r_mcbond_it 1.269 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.286 r_nbd_refined 0.249 r_symmetry_hbond_refined 0.207 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.152 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3214 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing