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Crystal structure of D-alanine-D-alanine ligase B from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EG0 PDB entry 4EG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 289 BupsA.00119.a.A1 PW25270 at 30.8 mg/mL against Wizard Full screen condition D2, 1 M NaK Tartrate, 0.1 M CHES pH 9.5, 0.2 M Li2SO4, crystal tracking ID 203378d2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.389 α = 84.47 b = 66.092 β = 80.5 c = 98.558 γ = 83.59
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97946 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 50 97.8 0.124 9.437 3.7 54908
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 96.6 0.546 3.1 2703
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 PDB entry 4EG0 2.2 35.27 54818 2772 97.02 0.2118 0.2097 0.2132 0.2503 0.2516 RANDOM 38.9073
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] -0.37 -0.04 1.48 -0.69 0.59 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.622 r_dihedral_angle_4_deg 18.491 r_dihedral_angle_3_deg 13.126 r_dihedral_angle_1_deg 5.395 r_angle_refined_deg 1.472 r_angle_other_deg 1.411 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.622 r_dihedral_angle_4_deg 18.491 r_dihedral_angle_3_deg 13.126 r_dihedral_angle_1_deg 5.395 r_angle_refined_deg 1.472 r_angle_other_deg 1.411 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8399 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction