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X-ray structure of the WlaRG aminotransferase from Campylobacter jejuni in complex with TDP-Qui3N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U1Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM MOPS (pH 7)
12-15% PEG3350
10 mM TDP-Qui3N
1 mM PLP
Crystal Properties Matthews coefficient Solvent content 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.824 α = 90 b = 56.644 β = 90.01 c = 124.549 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 CCD Bruker Platinum 135 montel 2016-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.45 50 98.2 0.076 0.076 9 3.2 261560
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.55 93.8 0.37 1.9 2 47910
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2u1z 1.45 29.92 248592 12952 98.16 0.12853 0.12724 0.1534 0.1497 RANDOM 12.901
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] 2.35 -1.23 2.34 -4.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.029 r_dihedral_angle_4_deg 16.852 r_dihedral_angle_3_deg 14.364 r_dihedral_angle_1_deg 6.772 r_long_range_B_refined 5.4 r_long_range_B_other 5.4 r_scangle_other 4.288 r_scbond_it 3.029 r_scbond_other 3.029 r_mcangle_it 2.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.029 r_dihedral_angle_4_deg 16.852 r_dihedral_angle_3_deg 14.364 r_dihedral_angle_1_deg 6.772 r_long_range_B_refined 5.4 r_long_range_B_other 5.4 r_scangle_other 4.288 r_scbond_it 3.029 r_scbond_other 3.029 r_mcangle_it 2.239 r_mcangle_other 2.239 r_mcbond_it 1.754 r_mcbond_other 1.751 r_angle_refined_deg 1.731 r_angle_other_deg 0.796 r_chiral_restr 0.114 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.001 r_bond_other_d 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 11791 Nucleic Acid Atoms Solvent Atoms 1593 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing