☰ Navigation Tabs
Crystal structure of Apo 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, 29% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.68 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.993 α = 90 b = 107.027 β = 90 c = 211.003 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 2013-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97949 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.25 50 100 0.09 9 14.6 66609
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 2.3 33.41 55129 2970 90.18 0.20605 0.20382 0.2063 0.24819 0.2473 RANDOM 46.076
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 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.57 r_dihedral_angle_4_deg 21.497 r_dihedral_angle_3_deg 15.553 r_long_range_B_refined 9.476 r_long_range_B_other 9.476 r_scangle_other 7.776 r_dihedral_angle_1_deg 5.956 r_mcangle_it 5.498 r_mcangle_other 5.498 r_scbond_other 5.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.57 r_dihedral_angle_4_deg 21.497 r_dihedral_angle_3_deg 15.553 r_long_range_B_refined 9.476 r_long_range_B_other 9.476 r_scangle_other 7.776 r_dihedral_angle_1_deg 5.956 r_mcangle_it 5.498 r_mcangle_other 5.498 r_scbond_other 5.078 r_scbond_it 5.077 r_mcbond_it 3.88 r_mcbond_other 3.879 r_angle_refined_deg 1.57 r_angle_other_deg 1.27 r_chiral_restr 0.088 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 8970 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling PHASER phasing