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High Resolution Crystal Structure of the Catalytic Domain of ADAMTS-5 (Aggrecanase-2)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 PEG 3350, ammonium acetate, pH 8.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.88 34.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.057 α = 90 b = 44.487 β = 90.07 c = 76.38 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 ADSC QUANTUM 210 mirror 2007-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 95.9 0.049 10 3.6 67485 67485 1 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.45 88.9 0.41 3.3 6226
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.4 26.53 67485 67471 3395 95.82 0.187 0.187 0.185 0.1832 0.214 0.2132 RANDOM 18.132
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] 1.24 0.16 -0.95 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.251 r_dihedral_angle_4_deg 20.402 r_dihedral_angle_3_deg 12.679 r_dihedral_angle_1_deg 7.267 r_scangle_it 3.005 r_scbond_it 1.889 r_mcangle_it 1.373 r_angle_refined_deg 1.257 r_mcbond_it 0.779 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.251 r_dihedral_angle_4_deg 20.402 r_dihedral_angle_3_deg 12.679 r_dihedral_angle_1_deg 7.267 r_scangle_it 3.005 r_scbond_it 1.889 r_mcangle_it 1.373 r_angle_refined_deg 1.257 r_mcbond_it 0.779 r_nbtor_refined 0.301 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.087 r_metal_ion_refined 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3336 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 68
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling