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Crystal structure of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae KACC10331
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NMP PDB ENTRY 2NMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 287 15%(w/v) PEG4000, 0.1M Tris, pH8.5, 0.2M MgCl2, 0.3M Dimethylethyl-(3-Sulfopropyl)-ammonium, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.01 38.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.043 α = 90 b = 83.043 β = 90 c = 97.601 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 2008-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.00000 Photon Factory BL-17A
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 50 99.9 23816 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.1 99.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2NMP 2 38.21 22572 22572 1217 99.92 0.19932 0.19932 0.19584 0.2104 0.26486 0.271 RANDOM 36.893
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] -0.08 -0.08 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.137 r_dihedral_angle_4_deg 20.097 r_dihedral_angle_3_deg 19.717 r_sphericity_free 10.371 r_dihedral_angle_1_deg 6.996 r_scangle_it 5.682 r_sphericity_bonded 5.027 r_scbond_it 3.935 r_rigid_bond_restr 2.834 r_mcangle_it 2.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.137 r_dihedral_angle_4_deg 20.097 r_dihedral_angle_3_deg 19.717 r_sphericity_free 10.371 r_dihedral_angle_1_deg 6.996 r_scangle_it 5.682 r_sphericity_bonded 5.027 r_scbond_it 3.935 r_rigid_bond_restr 2.834 r_mcangle_it 2.686 r_angle_refined_deg 2.002 r_mcbond_it 1.814 r_nbtor_refined 0.311 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.243 r_symmetry_hbond_refined 0.232 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.176 r_bond_refined_d 0.022 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2582 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing