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Crystal structure of LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana complexed with L-malate ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native LL-diaminopimelate aminotransferase structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 2.1M D,L-malic acid, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.587 α = 90 b = 102.587 β = 90 c = 172.939 γ = 120
Symmetry Space Group P 32 2 1
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 KOHZU: Double Crystal Si(111) 2006-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11590 ALS 8.3.1
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 2.4 20 90.4 0.083 13.5 4 37831 37831
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 93.6 0.553 1.9 3.7 3838
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 (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 Native LL-diaminopimelate aminotransferase structure 2.4 20 35896 35896 1916 90.16 0.18309 0.17956 0.1794 0.25073 0.2516 RANDOM 36.565
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] -1.16 -0.58 -1.16 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.465 r_dihedral_angle_4_deg 21.553 r_dihedral_angle_3_deg 21.136 r_dihedral_angle_1_deg 8.548 r_scangle_it 4.824 r_scbond_it 3.33 r_angle_refined_deg 2.374 r_mcangle_it 2.08 r_mcbond_it 1.259 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.465 r_dihedral_angle_4_deg 21.553 r_dihedral_angle_3_deg 21.136 r_dihedral_angle_1_deg 8.548 r_scangle_it 4.824 r_scbond_it 3.33 r_angle_refined_deg 2.374 r_mcangle_it 2.08 r_mcbond_it 1.259 r_nbtor_refined 0.318 r_symmetry_hbond_refined 0.271 r_nbd_refined 0.245 r_symmetry_vdw_refined 0.233 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.173 r_bond_refined_d 0.028 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6288 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing