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Crystal structure of ADP and D-alanyl-D-alanine complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 287 0.2M Sodium acetate, 0.1M ris pH7.0, 29% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.66 53.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.67 α = 90 b = 106.545 β = 90 c = 211.103 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 CCD ADSC QUANTUM 315r 2013-07-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.997 PAL/PLS 5C (4A)
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 2.4 50 100 0.09 32.4 7 56216
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.4 35.02 53293 2846 99.9 0.19874 0.19685 0.2 0.23376 0.2339 RANDOM 44.64
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.887 r_dihedral_angle_4_deg 20.547 r_dihedral_angle_3_deg 15.527 r_long_range_B_other 9.28 r_long_range_B_refined 9.279 r_scangle_other 7.266 r_dihedral_angle_1_deg 5.911 r_mcangle_it 5.319 r_mcangle_other 5.319 r_scbond_it 4.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.887 r_dihedral_angle_4_deg 20.547 r_dihedral_angle_3_deg 15.527 r_long_range_B_other 9.28 r_long_range_B_refined 9.279 r_scangle_other 7.266 r_dihedral_angle_1_deg 5.911 r_mcangle_it 5.319 r_mcangle_other 5.319 r_scbond_it 4.799 r_scbond_other 4.798 r_mcbond_it 3.638 r_mcbond_other 3.636 r_angle_refined_deg 1.617 r_angle_other_deg 1.319 r_chiral_restr 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.007 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 9108 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling PHASER phasing