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Crystal structure of the omega TRANSAMINASE FROM PSEUDOMONAS Jessenii in complex with PLP and 6-aminohexanoate (6-ACA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G4B D_1200009303
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 1.0 M Sodium succinate pH 7.5, 0.1 mM PLP
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98 α = 90 b = 98 β = 90 c = 119.76 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH 2015-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 51.1 100 0.07 7.9 4.1 41576 22.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 100 0.404 1.8 4
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 FOURIER SYNTHESIS THROUGHOUT D_1200009303 2.45 51.1 39421 2111 99.9 0.16666 0.16468 0.1717 0.20437 0.2059 RANDOM 37.574
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] -0.23 -0.23 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.109 r_dihedral_angle_4_deg 13.925 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_1_deg 6.081 r_long_range_B_refined 4.354 r_long_range_B_other 4.344 r_scangle_other 3.112 r_mcangle_other 2.118 r_mcangle_it 2.117 r_scbond_it 1.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.109 r_dihedral_angle_4_deg 13.925 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_1_deg 6.081 r_long_range_B_refined 4.354 r_long_range_B_other 4.344 r_scangle_other 3.112 r_mcangle_other 2.118 r_mcangle_it 2.117 r_scbond_it 1.898 r_scbond_other 1.898 r_mcbond_it 1.354 r_angle_refined_deg 1.345 r_mcbond_other 1.345 r_angle_other_deg 0.905 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 6936 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing