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Crystal structure of catalytic domain of TNF-alpha converting enzyme (TACE) with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BKC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 292 PEG 4000, isopropanol, NaCitrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.2 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.12 α = 90 b = 59.17 β = 90 c = 195.81 γ = 90
Symmetry Space Group P 21 21 21
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 2000-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
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 2.2 20 86.8 29248 25216
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 20 86.8
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 1bkc 2.28 20 26333 22637 1777 85.96 0.21584 0.21584 0.20993 0.2092 0.28506 0.2816 RANDOM 30.022
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] 1.44 -1.05 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.836 r_dihedral_angle_4_deg 17.196 r_dihedral_angle_3_deg 16.317 r_dihedral_angle_1_deg 5.991 r_scangle_it 2.655 r_scbond_it 1.703 r_angle_refined_deg 1.392 r_mcangle_it 1.204 r_mcbond_it 0.707 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.836 r_dihedral_angle_4_deg 17.196 r_dihedral_angle_3_deg 16.317 r_dihedral_angle_1_deg 5.991 r_scangle_it 2.655 r_scbond_it 1.703 r_angle_refined_deg 1.392 r_mcangle_it 1.204 r_mcbond_it 0.707 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.261 r_metal_ion_refined 0.247 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.115 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4100 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing