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Crystal Structure of the L322F mutant of Omega Transaminase TA_2799 from Pseudomonas putida KT2440
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9J2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.2M Lithium sulphate, 0.1M bis-Tris pH 5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.16 α = 90 b = 121.44 β = 111.88 c = 147.41 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 RAYONIX MX225HE 2023-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.9789 RRCAT INDUS-2 PX-BL21
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 2.5 40 98.8 0.18 8.71 3.89 133254
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 2.5 2.6 1.18
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.5 39.48 126588 6663 98.91 0.19621 0.19428 0.2001 0.23279 0.2342 RANDOM 39.907
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] -0.76 -1.03 1.58 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.887 r_dihedral_angle_2_deg 10.734 r_long_range_B_other 9.465 r_long_range_B_refined 9.464 r_scangle_other 7.752 r_mcangle_it 7.003 r_mcangle_other 7.003 r_dihedral_angle_1_deg 6.646 r_scbond_it 5.422 r_scbond_other 5.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.887 r_dihedral_angle_2_deg 10.734 r_long_range_B_other 9.465 r_long_range_B_refined 9.464 r_scangle_other 7.752 r_mcangle_it 7.003 r_mcangle_other 7.003 r_dihedral_angle_1_deg 6.646 r_scbond_it 5.422 r_scbond_other 5.422 r_mcbond_it 4.906 r_mcbond_other 4.906 r_angle_refined_deg 1.289 r_angle_other_deg 0.447 r_chiral_restr 0.061 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 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 27900 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing