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X-ray structure of the WlaRF aminotransferase from Campylobacter jejuni, K184A mutant 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% PEG-3350
1 mM PLP
10 mM TDP-Qui3N
Crystal Properties Matthews coefficient Solvent content 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.164 α = 90 b = 56.653 β = 90.04 c = 124.802 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 2016-08-21 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 1.6 50 97.6 0.065 0.065 10.2 3 194888
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 1.6 1.7 92.7 0.303 1.9 1.9
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 5u1z 1.6 29.98 185140 9738 97.41 0.13369 0.13222 0.1453 0.16132 0.1691 RANDOM 16.422
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] 7.16 -3.35 0.49 -7.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.728 r_dihedral_angle_4_deg 15.202 r_dihedral_angle_3_deg 13.88 r_dihedral_angle_1_deg 6.857 r_long_range_B_refined 5.615 r_long_range_B_other 5.615 r_scangle_other 4.254 r_scbond_it 3.002 r_scbond_other 3.001 r_mcangle_it 2.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.728 r_dihedral_angle_4_deg 15.202 r_dihedral_angle_3_deg 13.88 r_dihedral_angle_1_deg 6.857 r_long_range_B_refined 5.615 r_long_range_B_other 5.615 r_scangle_other 4.254 r_scbond_it 3.002 r_scbond_other 3.001 r_mcangle_it 2.586 r_mcangle_other 2.586 r_mcbond_it 2.05 r_mcbond_other 2.049 r_angle_refined_deg 1.829 r_angle_other_deg 0.855 r_chiral_restr 0.12 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 11714 Nucleic Acid Atoms Solvent Atoms 1594 Heterogen Atoms 227
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing