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Crystal structure of AMP 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 0.2 M sodium acetate, 0.1 M Bis-Tris pH 7.0, 29% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.64 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.585 α = 90 b = 106.071 β = 90 c = 210.769 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 2013-05-28 M SINGLE WAVELENGTH
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 1.7 50 99.9 0.07 50 14.8
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 THROUGHOUT 1.7 34.96 145553 7688 99.6 0.17868 0.17702 0.1881 0.20949 0.2176 RANDOM 30.533
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 35.586 r_dihedral_angle_4_deg 16.416 r_dihedral_angle_3_deg 13.411 r_long_range_B_refined 7.744 r_long_range_B_other 7.744 r_dihedral_angle_1_deg 6.285 r_scangle_other 6.252 r_scbond_it 4.289 r_scbond_other 4.288 r_mcangle_it 3.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.586 r_dihedral_angle_4_deg 16.416 r_dihedral_angle_3_deg 13.411 r_long_range_B_refined 7.744 r_long_range_B_other 7.744 r_dihedral_angle_1_deg 6.285 r_scangle_other 6.252 r_scbond_it 4.289 r_scbond_other 4.288 r_mcangle_it 3.713 r_mcangle_other 3.713 r_mcbond_it 2.816 r_mcbond_other 2.814 r_angle_refined_deg 2.179 r_angle_other_deg 0.942 r_chiral_restr 0.13 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 9296 Nucleic Acid Atoms Solvent Atoms 730 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling PHASER phasing