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Crystal Structure of Gamma-glutamyltranspeptidase from Escherichia coli Acyl-Enzyme Intermediate
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 5 277 12.5% PEG 4000, 0.2M magnesium sulfate, 5% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.68 54.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.8 α = 90 b = 126.7 β = 90 c = 128.9 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 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 1.8 50 100 0.063 8 120057 120057 1 1 16.7
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 1.8 1.86 100 0.348 8
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 1.8 46.42 119896 119896 6008 99.9 0.181 0.18 0.18 0.1799 0.2 0.2003 RANDOM 21.9
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] 7.75 -2.48 -5.27
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 2.75 c_scbond_it 1.94 c_mcangle_it 1.47 c_angle_deg 1.3 c_mcbond_it 1.01 c_improper_angle_d 0.84 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 2.75 c_scbond_it 1.94 c_mcangle_it 1.47 c_angle_deg 1.3 c_mcbond_it 1.01 c_improper_angle_d 0.84 c_bond_d 0.005 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 8227 Nucleic Acid Atoms Solvent Atoms 896 Heterogen Atoms 42
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing