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Structure of transaminase ATA-117 arRmut11 from Arthrobacter sp. KNK168 inhibited with 1-(4-Bromophenyl)-2-fluoroethylamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WWJ PDB ENTRY 3WWJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 22% (W/V) PEG 3350, 0.2 M MGCL2 IN 0.1 M BIS-TRIS PROPANE BUFFER PH 7.0.
Crystal Properties Matthews coefficient Solvent content 2.59 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.148 α = 90 b = 135.506 β = 100.4 c = 197.319 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 120 PIXEL DECTRIS PILATUS 2M 2015-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.81 48.52 99.4 0.06 15.5 4.2 105927 2
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 2.81 2.86 99.7 0.61 2.1 4.3
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 PDB ENTRY 3WWJ 2.81 194.08 100000 5274 99.3 0.21156 0.21012 0.2142 0.23866 0.2413 RANDOM 65.287
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] 2.56 1.23 3.12 -5.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.889 r_dihedral_angle_4_deg 21.024 r_dihedral_angle_3_deg 13.358 r_long_range_B_refined 10.696 r_long_range_B_other 10.696 r_mcangle_it 7.024 r_mcangle_other 7.024 r_scangle_other 6.881 r_dihedral_angle_1_deg 5.707 r_mcbond_it 4.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.889 r_dihedral_angle_4_deg 21.024 r_dihedral_angle_3_deg 13.358 r_long_range_B_refined 10.696 r_long_range_B_other 10.696 r_mcangle_it 7.024 r_mcangle_other 7.024 r_scangle_other 6.881 r_dihedral_angle_1_deg 5.707 r_mcbond_it 4.746 r_mcbond_other 4.745 r_scbond_it 4.674 r_scbond_other 4.674 r_angle_other_deg 1.659 r_angle_refined_deg 1.464 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 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 28934 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 300
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing