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Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with PLP-DAP: an external aldimine mimic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z20 PDB entry 2Z20
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 45% (NH4)2SO4, 0.1 M HEPES pH 7.5, 3% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.67 α = 90 b = 102.67 β = 90 c = 172.145 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 315 2007-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115872 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 1.9 40 94.1 0.053 78472 78472
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 1.9 1.97 66.1 0.256
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2Z20 1.9 39.5 74474 74474 3938 94.03 0.15847 0.15684 0.159 0.18905 RANDOM 24.995
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] -0.66 -0.33 -0.66 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.538 r_dihedral_angle_4_deg 19.997 r_dihedral_angle_3_deg 13.389 r_dihedral_angle_1_deg 5.654 r_scangle_it 3.815 r_scbond_it 2.43 r_mcangle_it 1.439 r_angle_refined_deg 1.328 r_mcbond_it 0.908 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.538 r_dihedral_angle_4_deg 19.997 r_dihedral_angle_3_deg 13.389 r_dihedral_angle_1_deg 5.654 r_scangle_it 3.815 r_scbond_it 2.43 r_mcangle_it 1.439 r_angle_refined_deg 1.328 r_mcbond_it 0.908 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6338 Nucleic Acid Atoms Solvent Atoms 754 Heterogen Atoms 89
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling