☰ Navigation Tabs
Crystal structure of K270Q variant of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with L-Glu: External aldimine form
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 2.75 55.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.676 α = 90 b = 102.676 β = 90 c = 172.014 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 2007-11-29 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 1.85 40 95.9 0.075 86778 86778
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) 1.85 1.92 95.9 0.653
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 1.85 39.5 82201 82201 4342 95.6 0.18773 0.18554 0.1874 0.22959 RANDOM 32.083
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] -0.61 -0.31 -0.61 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.854 r_dihedral_angle_4_deg 19.211 r_dihedral_angle_3_deg 16.281 r_dihedral_angle_1_deg 6.621 r_scangle_it 4.471 r_scbond_it 3.01 r_angle_refined_deg 1.853 r_mcangle_it 1.795 r_mcbond_it 1.141 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.854 r_dihedral_angle_4_deg 19.211 r_dihedral_angle_3_deg 16.281 r_dihedral_angle_1_deg 6.621 r_scangle_it 4.471 r_scbond_it 3.01 r_angle_refined_deg 1.853 r_mcangle_it 1.795 r_mcbond_it 1.141 r_nbtor_refined 0.314 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.137 r_chiral_restr 0.135 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 754 Heterogen Atoms 60
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling