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Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with DON
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XLU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 PEG 4000, 100 mM NaCl, 200 mM MgCl2, MPD, 100 mM Tris-Cl
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.56 α = 90 b = 61.396 β = 90 c = 145.81 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 IMAGE PLATE RIGAKU RAXIS IV++ 2017-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.15 35 97.1 0.024 29.39 10 29483
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 86.4 2.73 9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 5XLU 2.15 35 27909 1532 97.16 0.18026 0.17702 0.1847 0.23609 0.2392 RANDOM 40.59
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] -1.96 1.11 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.963 r_dihedral_angle_3_deg 15.343 r_dihedral_angle_4_deg 14.968 r_dihedral_angle_1_deg 6.996 r_long_range_B_other 5.948 r_long_range_B_refined 5.947 r_scangle_other 4.564 r_mcangle_it 4.298 r_mcangle_other 4.297 r_scbond_it 3.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.963 r_dihedral_angle_3_deg 15.343 r_dihedral_angle_4_deg 14.968 r_dihedral_angle_1_deg 6.996 r_long_range_B_other 5.948 r_long_range_B_refined 5.947 r_scangle_other 4.564 r_mcangle_it 4.298 r_mcangle_other 4.297 r_scbond_it 3.267 r_scbond_other 3.267 r_mcbond_other 3.119 r_mcbond_it 3.118 r_angle_refined_deg 1.662 r_angle_other_deg 1.553 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4104 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing PHASER phasing