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Crystal structure of LysN, alpha-aminoadipate aminotransferase (complexed with N-(5'-phosphopyridoxyl)-L-leucine), from Thermus thermophilus HB27
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DTV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 18% PEG 4000, 0.1M Tris-HCl (pH 7.0), 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.107 α = 90 b = 62.229 β = 116.34 c = 107.439 γ = 90
Symmetry Space Group C 1 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 4r mirrors 2007-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.978 Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 50 100 0.109 0.109 13.8 3.5 81957 81957 2 2 15.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 100 0.323 0.323 2.8 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2DTV 1.75 36.86 77545 4188 99.7 0.155 0.153 0.1662 0.194 0.1699 RANDOM 16.14
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] 0.03 -0.02 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.322 r_dihedral_angle_2_deg 7.839 r_long_range_B_refined 6.657 r_long_range_B_other 6.568 r_dihedral_angle_1_deg 6.221 r_scangle_other 5.574 r_scbond_it 3.701 r_scbond_other 3.701 r_mcangle_it 2.302 r_mcangle_other 2.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.322 r_dihedral_angle_2_deg 7.839 r_long_range_B_refined 6.657 r_long_range_B_other 6.568 r_dihedral_angle_1_deg 6.221 r_scangle_other 5.574 r_scbond_it 3.701 r_scbond_other 3.701 r_mcangle_it 2.302 r_mcangle_other 2.302 r_angle_refined_deg 2.181 r_mcbond_it 1.737 r_mcbond_other 1.737 r_angle_other_deg 0.723 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6127 Nucleic Acid Atoms Solvent Atoms 754 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing