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Crystal structure of L,L-diaminopimelate aminotransferase (DapL) from Verrucomicrobium spinosum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QGU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 281.15 60% v/v T-mate, 100 mM malic acid
Crystal Properties Matthews coefficient Solvent content 2.83 56.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.05 α = 90 b = 121.372 β = 102.01 c = 76.545 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS EIGER X 16M 2018-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95366 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.25 49.46 99.5 0.145 0.172 0.092 0.926 8.1 3.5 44544
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 95.7 1.334 1.583 0.843 0.335 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 3QGU 2.25 47.19 44427 2320 99.05 0.19088 0.18889 0.1955 0.232 0.2345 RANDOM 38.536
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] -0.32 0.11 0.07 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.089 r_dihedral_angle_4_deg 19.235 r_dihedral_angle_3_deg 14.839 r_long_range_B_refined 6.07 r_long_range_B_other 6.052 r_dihedral_angle_1_deg 6 r_scangle_other 3.509 r_mcangle_it 3.365 r_mcangle_other 3.365 r_scbond_it 2.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.089 r_dihedral_angle_4_deg 19.235 r_dihedral_angle_3_deg 14.839 r_long_range_B_refined 6.07 r_long_range_B_other 6.052 r_dihedral_angle_1_deg 6 r_scangle_other 3.509 r_mcangle_it 3.365 r_mcangle_other 3.365 r_scbond_it 2.124 r_scbond_other 2.124 r_mcbond_it 2.03 r_mcbond_other 2.029 r_angle_refined_deg 1.281 r_angle_other_deg 1.159 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 6215 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing Coot model building