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de novo crystal structure of the Pyrococcus Furiosus TET3 aminopeptidase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 293 drop : 1.5 ul of protein+1.5 ul reservoir (HEPES 0.1 M pH 7.7, NH4CH3COO 0.2 M, 2 mM CoCl2, MPD 44%) +1.5 Gd-DO3A 300 mM
Crystal Properties Matthews coefficient Solvent content 2.55 51.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 203.908 α = 90 b = 203.908 β = 90 c = 112.443 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.71081 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.5 48.062 96.1 0.192 0.04 0.998 14.6 22.1 39432 44.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 77.4 1.248 0.422 0.481 1.9 9.2 3500
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD FREE R-VALUE 2.5 48.062 1.35 39419 1982 96 0.1802 0.1781 0.1793 0.2184 0.2173 Random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.273 f_angle_d 1.281 f_chiral_restr 0.06 f_bond_d 0.016 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7863 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement XDS data reduction SHELX phasing PDB_EXTRACT data extraction Aimless data scaling