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Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 285 20% PEG 400, 0.1M Tris 8.5, 0.2M magnesium chloride, 0.3 M dimethylethyl-(3-sulfopropyl)-ammonium, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.04 39.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.236 α = 90 b = 83.236 β = 90 c = 98.277 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 210 2010-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 0.96418 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 2.1 50 20817
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.1 38.32 20817 19620 1063 99.66 0.20821 0.2045 0.2127 0.28249 0.2858 RANDOM 35.921
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 38.843 r_dihedral_angle_4_deg 22.605 r_dihedral_angle_3_deg 18.615 r_dihedral_angle_1_deg 7.776 r_scangle_it 5.112 r_scbond_it 3.137 r_mcangle_it 2.059 r_angle_refined_deg 1.989 r_mcbond_it 1.154 r_chiral_restr 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.843 r_dihedral_angle_4_deg 22.605 r_dihedral_angle_3_deg 18.615 r_dihedral_angle_1_deg 7.776 r_scangle_it 5.112 r_scbond_it 3.137 r_mcangle_it 2.059 r_angle_refined_deg 1.989 r_mcbond_it 1.154 r_chiral_restr 0.144 r_bond_refined_d 0.021 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 2597 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 28
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling