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Crystal Structure of Gamma-glutamyltranspeptidase from Escherichia coli (monoclinic form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DBU A MOLECULE (CHAIN ID A,B) OF THE PDB ENTRY 2DBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 20% PEG 4000, 0.2M calcium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.6 52.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.23 α = 90 b = 127.9 β = 94.78 c = 75.14 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 100 CCD RIGAKU JUPITER 210 2006-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 1.95 50 98.2 0.095 9.2 3.2 89113 89113 1 1
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) 1.95 2.02 96.4 0.317 3 8681
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 MOLECULAR REPLACEMENT THROUGHOUT A MOLECULE (CHAIN ID A,B) OF THE PDB ENTRY 2DBU 1.95 29.91 83076 83076 4165 93.1 0.195 0.195 0.193 0.194 0.231 0.2296 RANDOM 14.965
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 r_dihedral_angle_2_deg 37.079 r_dihedral_angle_4_deg 15.131 r_dihedral_angle_3_deg 14.655 r_dihedral_angle_1_deg 6.036 r_scangle_it 2.878 r_scbond_it 1.905 r_angle_refined_deg 1.256 r_mcangle_it 1.029 r_mcbond_it 0.715 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.079 r_dihedral_angle_4_deg 15.131 r_dihedral_angle_3_deg 14.655 r_dihedral_angle_1_deg 6.036 r_scangle_it 2.878 r_scbond_it 1.905 r_angle_refined_deg 1.256 r_mcangle_it 1.029 r_mcbond_it 0.715 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.201 r_metal_ion_refined 0.136 r_xyhbond_nbd_refined 0.107 r_symmetry_hbond_refined 0.089 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8099 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction BSS data collection HKL-2000 data reduction