☰ Navigation Tabs
Crystal structure of the DABA transaminase EctB from the halophilic and cold-adapted Marinobacter sp. CK1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 0.1M bisTRIS propane pH 8,
0.2 M disodium malonate,
19.6 % PEG3350 (w/v).
Crystal Properties Matthews coefficient Solvent content 2.34 47.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.648 α = 90 b = 99.332 β = 104.82 c = 112.698 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 100 PIXEL DECTRIS PILATUS3 2M 2022-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 45.53 99.6 0.089 0.991 5.8 1.9 115468
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 99.7 0.773 0.451 1 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 40.13 109707 5736 99.55 0.16752 0.1654 0.20815 0.2129 RANDOM 38.475
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] -1.55 0.67 0.64 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.819 r_dihedral_angle_3_deg 13.462 r_long_range_B_refined 6.988 r_long_range_B_other 6.966 r_dihedral_angle_1_deg 6.677 r_scangle_other 6.14 r_scbond_it 4.372 r_scbond_other 4.372 r_mcangle_it 3.621 r_mcangle_other 3.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.819 r_dihedral_angle_3_deg 13.462 r_long_range_B_refined 6.988 r_long_range_B_other 6.966 r_dihedral_angle_1_deg 6.677 r_scangle_other 6.14 r_scbond_it 4.372 r_scbond_other 4.372 r_mcangle_it 3.621 r_mcangle_other 3.62 r_mcbond_it 2.897 r_mcbond_other 2.897 r_angle_refined_deg 2.177 r_angle_other_deg 0.74 r_chiral_restr 0.115 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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 12768 Nucleic Acid Atoms Solvent Atoms 641 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction