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T391A precursor mutant protein of gamma-Glutamyltranspeptidase from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DBU A MOLECULE (CHAIN ID A,B) OF PDB ENTRY 2DBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 18% PEG 4000, 10% iso-propanol, 0.1M sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.6 α = 90 b = 134.6 β = 90 c = 118.4 γ = 90
Symmetry Space Group P 43 21 2
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 2006-04-16 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 2.55 50 92.7 0.092 11.2 12 33506 33506 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 2.55 2.64 91.9 0.314 11.4 3262
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 PDB ENTRY 2DBU 2.55 30 30764 30764 1521 92.01 0.22 0.22 0.217 0.2111 0.27 0.2608 RANDOM 42.856
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.761 r_dihedral_angle_3_deg 19.151 r_dihedral_angle_4_deg 17.815 r_dihedral_angle_1_deg 6.52 r_scangle_it 1.615 r_angle_refined_deg 1.282 r_scbond_it 1.022 r_mcangle_it 0.705 r_mcbond_it 0.402 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.761 r_dihedral_angle_3_deg 19.151 r_dihedral_angle_4_deg 17.815 r_dihedral_angle_1_deg 6.52 r_scangle_it 1.615 r_angle_refined_deg 1.282 r_scbond_it 1.022 r_mcangle_it 0.705 r_mcbond_it 0.402 r_nbtor_refined 0.303 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.182 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7415 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
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 HKL-2000 data scaling