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Crystal Structure of Gamma-glutamyltranspeptidase from Escherichia coli Complexed with L-Glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DBU PDB ENTRY 2DBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 12.5% PEG 4000, 0.2M calcium chloride, 0.1M Tris-HCl, 50mM L-glutamate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.64 53.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.7 α = 90 b = 126.5 β = 90 c = 129.2 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 4 2005-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000, 0.9000 SPring-8 BL41XU
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 1.68 50 99.8 0.112 5.7 144777 144777 1 1 22.6
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 1.68 1.74 99.7 0.336 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2DBU 1.7 46.24 139781 139781 7015 99.5 0.195 0.194 0.194 0.1945 0.212 0.2132 RANDOM 26.8
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] 8.2 -3.61 -4.59
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.19 c_scbond_it 2.23 c_angle_deg 2.2 c_mcangle_it 1.61 c_mcbond_it 1.1 c_improper_angle_d 0.86 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.19 c_scbond_it 2.23 c_angle_deg 2.2 c_mcangle_it 1.61 c_mcbond_it 1.1 c_improper_angle_d 0.86 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8136 Nucleic Acid Atoms Solvent Atoms 795 Heterogen Atoms 28
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing