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Crystal Structure of Eukaryotic Hydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 293 0.032 M ammonium citrate tribasic (pH 7.0), 0.02 M MES monohydrate, 0.016 M imidazole, 0.002 M zinc sulfate heptahydrate, 0.128 M potassium thiocyanate, 12.8% w/v polyethylene glycol 3,350, 3.2% w/v polyethylene glycol monomethyl ether 2,000, and 5% w/v polyethylene glycol monomethyl ether 550
Crystal Properties Matthews coefficient Solvent content 2.78 55.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.06 α = 90 b = 96.576 β = 115.04 c = 89.282 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 80 CCD MARMOSAIC 300 mm CCD 2016-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.978 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.48 50 100 19.5 6.4 44255
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2cbj 2.481 44.249 1.35 40939 2013 91.49 0.1838 0.1811 0.1841 0.2357 0.2397
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 18.452 f_angle_d 1.126 f_chiral_restr 0.058 f_bond_d 0.01 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6905 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PHENIX phasing