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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 protein code 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 1.87 34.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.818 α = 90 b = 44.491 β = 90.26 c = 76.655 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 ADSC QUANTUM 210 2007-06-13 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 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 30 99.5 0.06 24.1 3.6 70408 70056 -1.5 -3 11.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.45 97.3 0.259 3.3 3.3 6795
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 protein code 3B8Z 1.4 26.41 66502 3536 99.56 0.18236 0.18084 0.1797 0.2103 0.2096 RANDOM 15.837
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] 0.8 -0.16 -0.64 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.428 r_dihedral_angle_4_deg 19.795 r_dihedral_angle_3_deg 13.098 r_dihedral_angle_1_deg 5.59 r_scangle_it 3.14 r_scbond_it 2.046 r_mcangle_it 1.451 r_angle_refined_deg 1.375 r_mcbond_it 0.855 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.428 r_dihedral_angle_4_deg 19.795 r_dihedral_angle_3_deg 13.098 r_dihedral_angle_1_deg 5.59 r_scangle_it 3.14 r_scbond_it 2.046 r_mcangle_it 1.451 r_angle_refined_deg 1.375 r_mcbond_it 0.855 r_nbtor_refined 0.302 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.16 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.09 r_metal_ion_refined 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3336 Nucleic Acid Atoms Solvent Atoms 587 Heterogen Atoms 62
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling