☰ Navigation Tabs
Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E5N PDB ENTRY 3E5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 283 0.001ml of 6 mg/ml protein was mixed to 0.001ml of a mother liquor, containing 30%(w/v) PEG 4000, 0.1M Tris pH 8.0, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.01 38.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.225 α = 90 b = 83.225 β = 90 c = 97.143 γ = 90
Symmetry Space Group P 43 21 2
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 270 2008-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.00000 PAL/PLS 4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.07 50 99.8 21461
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3E5N 2.07 41.95 20294 1097 99.96 0.235 0.21134 0.20793 0.27669 0.2422 RANDOM 39.19
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.771 r_dihedral_angle_4_deg 25.896 r_dihedral_angle_3_deg 19.745 r_dihedral_angle_1_deg 7.522 r_scangle_it 5.277 r_scbond_it 3.276 r_mcangle_it 2.228 r_angle_refined_deg 2.098 r_mcbond_it 1.281 r_chiral_restr 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.771 r_dihedral_angle_4_deg 25.896 r_dihedral_angle_3_deg 19.745 r_dihedral_angle_1_deg 7.522 r_scangle_it 5.277 r_scbond_it 3.276 r_mcangle_it 2.228 r_angle_refined_deg 2.098 r_mcbond_it 1.281 r_chiral_restr 0.147 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2586 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement