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Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex with an Amino-2-indanol compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B8Z PDB ENTRY 3B8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 25% PEG 3350, 200 mM ammonium acetate, 100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.83 32.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.692 α = 90 b = 44.444 β = 90.19 c = 76.458 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 110 CCD MAR CCD 165 mm 2007-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 2.02 50 99.8 0.044 0.044 29.1 3.6 23498 23451 -1.5 -3 19.2
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) 2.02 2.09 98.2 0.098 0.098 7.8 2.1 2238
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3B8Z 2.02 31.02 22235 1205 99.74 0.16321 0.15912 0.1597 0.23793 0.2362 RANDOM 20.495
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] 1.62 0.16 -1.33 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.693 r_dihedral_angle_4_deg 19.154 r_dihedral_angle_3_deg 15.648 r_dihedral_angle_1_deg 5.865 r_scangle_it 2.939 r_scbond_it 1.882 r_angle_refined_deg 1.354 r_mcangle_it 1.349 r_mcbond_it 0.772 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.693 r_dihedral_angle_4_deg 19.154 r_dihedral_angle_3_deg 15.648 r_dihedral_angle_1_deg 5.865 r_scangle_it 2.939 r_scbond_it 1.882 r_angle_refined_deg 1.354 r_mcangle_it 1.349 r_mcbond_it 0.772 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.105 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3350 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 72
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling