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The crystal structure of glutamate-bound human gamma-glutamyltranspeptidase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GDX pdb entry 4GDX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 15-25% PEG3350, 100 mM Ammonium chloride, 0.5 mM L-glutamate, 100 mM Na:Cacodylate pH 6.0 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.85 56.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.717 α = 90 b = 126.753 β = 90 c = 104.629 γ = 90
Symmetry Space Group C 2 2 21
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 2011-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 47.18 97.2 0.108 0.108 31.3 18.5 35539 34317 2 2 36.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 75.8 0.563 0.563 3.6 10.7
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 4GDX 2.21 43.975 1.99 35537 32579 1716 96.15 0.142 0.1398 0.1833 0.1837
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 13.606 f_angle_d 1.343 f_chiral_restr 0.076 f_bond_d 0.012 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4024 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms 99
Software Software Software Name Purpose PROTEUM PLUS data collection PHENIX model building PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing