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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
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 1.81 32.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.398 α = 90 b = 44.518 β = 90 c = 76.251 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 110 IMAGE PLATE MAR scanner 300 mm plate 2008-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 1.0 APS 21-ID-G
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 1.6 50 96 0.073 17.6 5.2 20954 20120 -1.5 -3 11.94
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) 1.6 1.66 65.8 0.356 2.2 2.8 1542
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 3B8Z 1.6 38.12 19840 1070 88.06 0.16137 0.15941 0.1659 0.19838 0.205 RANDOM 10.354
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] 0.62 -0.7 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.705 r_dihedral_angle_4_deg 17.564 r_dihedral_angle_3_deg 13.844 r_dihedral_angle_1_deg 5.83 r_scangle_it 3.082 r_scbond_it 1.962 r_mcangle_it 1.526 r_angle_refined_deg 1.442 r_angle_other_deg 0.967 r_mcbond_it 0.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.705 r_dihedral_angle_4_deg 17.564 r_dihedral_angle_3_deg 13.844 r_dihedral_angle_1_deg 5.83 r_scangle_it 3.082 r_scbond_it 1.962 r_mcangle_it 1.526 r_angle_refined_deg 1.442 r_angle_other_deg 0.967 r_mcbond_it 0.937 r_symmetry_vdw_other 0.257 r_nbd_refined 0.221 r_mcbond_other 0.213 r_nbd_other 0.203 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.183 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.153 r_nbtor_other 0.084 r_chiral_restr 0.082 r_metal_ion_refined 0.081 r_xyhbond_nbd_other 0.068 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1687 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 43
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling