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Crystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP and D-Ala-D-Ala
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other see publication
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.05 to 0.3 M Li2SO4, 0.1 M Bis-Tris pH 5.5 and 15-30% (w/v) PEG 3350, ratio protein:reservoir 1:1
Crystal Properties Matthews coefficient Solvent content 2.23 44.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.642 α = 90 b = 61.133 β = 90.31 c = 69.972 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 80 PIXEL DECTRIS PILATUS3 S 6M 2015-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.917410 Diamond I04-1
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 1.5 69.97 96.6 10.5 3.1 90609
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 see publication 1.5 69.97 86139 4448 96.25 0.13616 0.13253 0.1416 0.20767 0.2108 RANDOM 26.004
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] -1.69 -1.4 0.86 0.85
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.121 r_dihedral_angle_2_deg 31.011 r_sphericity_bonded 21.439 r_dihedral_angle_4_deg 19.851 r_dihedral_angle_3_deg 14.824 r_long_range_B_refined 8.435 r_long_range_B_other 8.435 r_scangle_other 7.68 r_dihedral_angle_1_deg 7.129 r_mcangle_it 6.758
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.121 r_dihedral_angle_2_deg 31.011 r_sphericity_bonded 21.439 r_dihedral_angle_4_deg 19.851 r_dihedral_angle_3_deg 14.824 r_long_range_B_refined 8.435 r_long_range_B_other 8.435 r_scangle_other 7.68 r_dihedral_angle_1_deg 7.129 r_mcangle_it 6.758 r_mcangle_other 6.758 r_scbond_it 6.683 r_scbond_other 6.679 r_mcbond_it 5.652 r_mcbond_other 5.652 r_rigid_bond_restr 4.984 r_angle_refined_deg 2.583 r_angle_other_deg 1.432 r_chiral_restr 0.174 r_bond_refined_d 0.027 r_gen_planes_refined 0.014 r_gen_planes_other 0.005 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4678 Nucleic Acid Atoms Solvent Atoms 789 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing