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Crystal structure of apo-LL-diaminopimelate aminotransferase from Arabidopsis thaliana (no PLP)
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 2.77 55.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.101 α = 90 b = 103.101 β = 90 c = 171.827 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 2007-06-27 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 1.99 40 100 0.078 73013 73013
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) 1.99 2.06 100 0.797
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 PDB entry 2Z20 1.99 38.72 69256 69256 3680 99.9 0.19125 0.18921 0.1856 0.2293 0.223 RANDOM 36.888
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] -0.77 -0.38 -0.77 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.821 r_dihedral_angle_4_deg 16.327 r_dihedral_angle_3_deg 15.746 r_dihedral_angle_1_deg 6.333 r_scangle_it 4.57 r_scbond_it 2.859 r_mcangle_it 2.066 r_angle_refined_deg 1.551 r_mcbond_it 1.127 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.821 r_dihedral_angle_4_deg 16.327 r_dihedral_angle_3_deg 15.746 r_dihedral_angle_1_deg 6.333 r_scangle_it 4.57 r_scbond_it 2.859 r_mcangle_it 2.066 r_angle_refined_deg 1.551 r_mcbond_it 1.127 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 6338 Nucleic Acid Atoms Solvent Atoms 629 Heterogen Atoms 10
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling