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Crystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP
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 2.24 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.648 α = 90 b = 61.15 β = 90.17 c = 70.079 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 1.3 70.08 97.6 15 4.8 141049
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 1.3 70.08 133936 7097 97.58 0.14825 0.14591 0.1556 0.19007 0.1995 RANDOM 24.763
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] -0.98 1.52 0.64 0.33
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.426 r_dihedral_angle_2_deg 30.341 r_dihedral_angle_4_deg 20.523 r_sphericity_bonded 19.534 r_dihedral_angle_3_deg 13.802 r_dihedral_angle_1_deg 7.711 r_long_range_B_refined 7.277 r_long_range_B_other 7.276 r_scangle_other 6.253 r_scbond_other 5.386
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.426 r_dihedral_angle_2_deg 30.341 r_dihedral_angle_4_deg 20.523 r_sphericity_bonded 19.534 r_dihedral_angle_3_deg 13.802 r_dihedral_angle_1_deg 7.711 r_long_range_B_refined 7.277 r_long_range_B_other 7.276 r_scangle_other 6.253 r_scbond_other 5.386 r_scbond_it 5.385 r_rigid_bond_restr 4.711 r_mcangle_other 4.583 r_mcangle_it 4.581 r_mcbond_it 3.726 r_mcbond_other 3.716 r_angle_refined_deg 2.247 r_angle_other_deg 1.444 r_chiral_restr 0.184 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 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 4672 Nucleic Acid Atoms Solvent Atoms 785 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing