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Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with Azaserine
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 NH4Cl, 100 mM TrisCl pH 8.0, 5mM azaserine
Crystal Properties Matthews coefficient Solvent content 2.11 41.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.164 α = 90 b = 60.016 β = 100.42 c = 74.781 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 MARMOSAIC 225 mm CCD 2016-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97872 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.97 73.55 97.9 16.8 6 35250
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 2.07 85.5 2.21 4.7
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 1.97 42.12 33530 1706 96.63 0.14587 0.14342 0.1539 0.19401 0.2014 RANDOM 25.288
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] 2.33 1.6 -2.29 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.114 r_dihedral_angle_3_deg 13.875 r_dihedral_angle_4_deg 12.801 r_dihedral_angle_1_deg 7.089 r_long_range_B_refined 5.044 r_long_range_B_other 4.997 r_scangle_other 3.581 r_mcangle_it 2.378 r_mcangle_other 2.378 r_scbond_it 2.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.114 r_dihedral_angle_3_deg 13.875 r_dihedral_angle_4_deg 12.801 r_dihedral_angle_1_deg 7.089 r_long_range_B_refined 5.044 r_long_range_B_other 4.997 r_scangle_other 3.581 r_mcangle_it 2.378 r_mcangle_other 2.378 r_scbond_it 2.375 r_scbond_other 2.375 r_mcbond_it 1.679 r_mcbond_other 1.679 r_angle_refined_deg 1.524 r_angle_other_deg 1.394 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4153 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building