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ADAM-8 metalloproteinase domain with bound batimastat
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R55 PDB ENTRY 1R55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 Purified ADAM-8/batimastat complex (10mg/mL) was crystallized by the sitting-drop vapor diffusion method, mixing 1uL complex with 1uL of 0.1M Tris pH 8.0, 1M sodium formate, 10% methanol. Crystals reached usable size in 10 days. Crystals were then transferred to a cryo solution containing 0.1M Tris pH 8.0, 1.2M sodium formate, 10% methanol, and 10% glycerol. The crystals were harvested and flash frozen in liquid nitrogen for data collection., VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.28 46.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.6 α = 90 b = 50.9 β = 102.4 c = 93.5 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 315r mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1 ALS 5.0.1
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 2.1 50 99.3 0.106 10.9 3.6 49827 49479 -3 -3
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 2.1 2.18 95.9 0.365 2.92 2.8 4746
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT R-free PDB ENTRY 1R55 2.1 44.745 1 49479 47689 2368 96.04 0.1916 0.1881 0.255 0.2626 random
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] 3.3066 -12.629 -4.8035 1.4969
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.89 f_angle_d 0.682 f_chiral_restr 0.049 f_bond_d 0.008 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6270 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 150
Software Software Software Name Purpose ADSC data collection MOLREP phasing PHENIX refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling