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Crystal structure of D-alanine-D-alanine ligase from Burkholderia xenovorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EG0 pdb entry 3eg0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Qiagen JCSG Core1 screen d5: 20% PEG 3350, 200mM LiCl; BuxeA.00119.a.A1 PS01358 at 23.2mg/ml, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.93 α = 90 b = 78.93 β = 90 c = 224.74 γ = 90
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 RIGAKU SATURN 944+ 2012-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.3 50 97.8 0.078 10.11 2.5 60791 59426 -3 36.882
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 99.3 0.478 0.478 2.09 2.4 4463
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3eg0 2.3 49.99 60791 59384 3006 97.8 0.2254 0.2254 0.2236 0.2216 0.2597 0.259 RANDOM 32.5859
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] 0.45 0.45 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.944 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_3_deg 13.747 r_dihedral_angle_1_deg 5.94 r_angle_refined_deg 1.698 r_angle_other_deg 1.473 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.944 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_3_deg 13.747 r_dihedral_angle_1_deg 5.94 r_angle_refined_deg 1.698 r_angle_other_deg 1.473 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8047 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms
Software Software Software Name Purpose JDirector data collection PHASER phasing REFMAC refinement XSCALE data scaling