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Crystal structure of the samarium derivative of mature gamma-glutamyltranspeptidase from Escherichia coli
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 8 277 15% PEG 4000, 0.2M calcium chloride, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.66 53.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.92 α = 90 b = 125.9 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 315 2005-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.2000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.02 50 99.9 0.065 5.3 84609 1 1 17.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.09 99.5 0.285 5.1 16196
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 2.02 50 83871 83871 4237 98.8 0.196 0.196 0.195 0.19 0.224 0.2174 RANDOM 27.8
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] 5.17 -1.53 -3.64
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 3.04 c_scbond_it 2.15 c_mcangle_it 1.85 c_angle_deg 1.3 c_mcbond_it 1.23 c_improper_angle_d 0.84 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8099 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 32
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction BSS data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing