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Crystal structure of tolloid-like protease 1 (TLL-1) protease domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 277 25% PEG 3350, 200mM lithium sulphate, 100mM Bis-Tris-HCl, pH 7.5, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.281 α = 90 b = 58.923 β = 104.62 c = 47.444 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 MARMOSAIC 225 mm CCD 2007-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.4 58.9 96.3 0.073 0.044 15.9 3.5 43398 41793 -3 20.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.44 74.1 0.479 0.327 2.9 2.66 2592
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 1DLE 1.4 29.96 41791 2090 96.39 0.155 0.154 0.1533 0.182 0.1792 RANDOM 18.521
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] -0.14 -0.08 0.11 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.716 r_dihedral_angle_4_deg 16.797 r_dihedral_angle_3_deg 12.887 r_sphericity_free 7.68 r_dihedral_angle_1_deg 6.135 r_sphericity_bonded 5.158 r_scangle_it 5.07 r_scbond_it 4.873 r_rigid_bond_restr 4.479 r_mcangle_it 2.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.716 r_dihedral_angle_4_deg 16.797 r_dihedral_angle_3_deg 12.887 r_sphericity_free 7.68 r_dihedral_angle_1_deg 6.135 r_sphericity_bonded 5.158 r_scangle_it 5.07 r_scbond_it 4.873 r_rigid_bond_restr 4.479 r_mcangle_it 2.747 r_mcbond_it 1.843 r_angle_refined_deg 1.473 r_symmetry_hbond_refined 0.591 r_symmetry_vdw_refined 0.365 r_nbtor_refined 0.312 r_nbd_refined 0.288 r_xyhbond_nbd_refined 0.256 r_chiral_restr 0.103 r_metal_ion_refined 0.034 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1598 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 24
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction