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crystal structure of the Pcryo_0618 aminotransferase from Psychrobacter cryohalolentis K5 in the presence of its internal aldimine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 Protein incubated with 5 mM UDP and 5 mM PLP. Precipitant: 18-22% PEG 5000, 200 mM tetraethylammonium chloride, and 100 mM Homo-PIPES (pH 5)
Crystal Properties Matthews coefficient Solvent content 3.61 65.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.019 α = 90 b = 157.97 β = 90 c = 130.591 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL Bruker PHOTON II 2019-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 50 99.2 0.091 12.5 10.2 80593
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 97.3 0.46 2.4 5.1
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 32.65 76621 3972 99.24 0.19927 0.19753 0.2042 0.23276 0.2382 RANDOM 22.965
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.327 r_dihedral_angle_2_deg 13.258 r_long_range_B_refined 7.019 r_long_range_B_other 7.019 r_dihedral_angle_1_deg 6.61 r_scangle_other 5.24 r_scbond_it 3.234 r_scbond_other 3.234 r_mcangle_it 3.209 r_mcangle_other 3.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.327 r_dihedral_angle_2_deg 13.258 r_long_range_B_refined 7.019 r_long_range_B_other 7.019 r_dihedral_angle_1_deg 6.61 r_scangle_other 5.24 r_scbond_it 3.234 r_scbond_other 3.234 r_mcangle_it 3.209 r_mcangle_other 3.209 r_mcbond_it 2.087 r_mcbond_other 2.084 r_angle_refined_deg 1.609 r_angle_other_deg 0.5 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 5784 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing