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Crystal structure of ADP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZQI
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 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.872 α = 90 b = 106.475 β = 90 c = 211.462 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 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9997 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 2.28 50 99.9 0.08 33.5 7.21 64040
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 4ZQI 2.28 37.51 62408 3336 99.96 0.18895 0.18555 0.1912 0.25288 0.2529 RANDOM 37.005
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.962 r_dihedral_angle_4_deg 22.068 r_dihedral_angle_3_deg 16.333 r_long_range_B_refined 7.937 r_long_range_B_other 7.937 r_dihedral_angle_1_deg 6.255 r_scangle_other 5.987 r_mcangle_it 4.455 r_mcangle_other 4.455 r_scbond_it 3.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.962 r_dihedral_angle_4_deg 22.068 r_dihedral_angle_3_deg 16.333 r_long_range_B_refined 7.937 r_long_range_B_other 7.937 r_dihedral_angle_1_deg 6.255 r_scangle_other 5.987 r_mcangle_it 4.455 r_mcangle_other 4.455 r_scbond_it 3.826 r_scbond_other 3.824 r_mcbond_it 2.95 r_mcbond_other 2.945 r_angle_refined_deg 1.769 r_angle_other_deg 0.843 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 9086 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling PHASER phasing