☰ Navigation Tabs
High Resolution Crystal Structure of Bacillus Licheniformis Gamma Glutamyl Transpeptidase with Acivicin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OTT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 PEG MME 2000, 200mM magnesium chloride, 100mM Tris-Cl, 5mM acivicin
VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.005 α = 90 b = 85.732 β = 90 c = 124.664 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++ 2016-06-01 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) 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 1.45 70.64 96.1 34.01 9.5 92246 24.9
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 1.45 1.48
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 4OTT 1.45 70.64 87318 4567 95.6 0.17508 0.17352 0.1731 0.20513 0.2052 RANDOM 15.915
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] 0.02 -0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.997 r_dihedral_angle_4_deg 13.902 r_dihedral_angle_3_deg 12.395 r_dihedral_angle_1_deg 6.783 r_long_range_B_refined 5.81 r_long_range_B_other 5.761 r_scangle_other 3.745 r_scbond_it 2.639 r_scbond_other 2.639 r_angle_refined_deg 2.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.997 r_dihedral_angle_4_deg 13.902 r_dihedral_angle_3_deg 12.395 r_dihedral_angle_1_deg 6.783 r_long_range_B_refined 5.81 r_long_range_B_other 5.761 r_scangle_other 3.745 r_scbond_it 2.639 r_scbond_other 2.639 r_angle_refined_deg 2.171 r_mcangle_it 1.832 r_mcangle_other 1.832 r_mcbond_it 1.343 r_mcbond_other 1.322 r_angle_other_deg 1.104 r_chiral_restr 0.142 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 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 4168 Nucleic Acid Atoms Solvent Atoms 817 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing PHASER model building