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X-ray structure of the Pcryo_0638 aminotransferase from Psychrobacter cryohalolentis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FRK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 18-22% PEG-8000, 200 mM tetramethylammonium chloride.
protein incubated with 1 mM PLP and 5 mM UDP-2-acetamido-4-amino-2,4,6-trideoxy-D-glucose
Crystal Properties Matthews coefficient Solvent content 2.55 51.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.529 α = 81.747 b = 63.141 β = 78.593 c = 69.853 γ = 66.818
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 2018-12-07 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 1.3 50 92.9 0.057 7.2 2.4 202026
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 1.3 1.4 83 0.229 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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3frk 1.3 29.957 202026 10084 92.941 0.151 0.1499 0.1692 0.1793 12.793
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] 0.478 -0.142 0.052 -0.374 -0.116 -0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.387 r_dihedral_angle_4_deg 15.917 r_dihedral_angle_3_deg 12.467 r_dihedral_angle_1_deg 7.083 r_lrange_it 5.451 r_lrange_other 5.451 r_scangle_it 3.052 r_scangle_other 3.051 r_scbond_it 2.021 r_scbond_other 2.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.387 r_dihedral_angle_4_deg 15.917 r_dihedral_angle_3_deg 12.467 r_dihedral_angle_1_deg 7.083 r_lrange_it 5.451 r_lrange_other 5.451 r_scangle_it 3.052 r_scangle_other 3.051 r_scbond_it 2.021 r_scbond_other 2.021 r_mcangle_it 1.862 r_mcangle_other 1.862 r_angle_other_deg 1.496 r_angle_refined_deg 1.472 r_mcbond_it 1.194 r_mcbond_other 1.192 r_xyhbond_nbd_refined 0.232 r_nbd_refined 0.227 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_other 0.208 r_symmetry_xyhbond_nbd_other 0.198 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.174 r_symmetry_nbd_refined 0.157 r_metal_ion_refined 0.139 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6166 Nucleic Acid Atoms Solvent Atoms 1280 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing