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Crystal structure of a heterooligomeric aminotransferase from Serratia sp. ATCC 39006, PMP-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8Y96
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 293 dipotassium hydrogenphosphate, sodium dihydrogenphosphate, lithium sulfate, CAPS
Crystal Properties Matthews coefficient Solvent content 2.92 57.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.465 α = 90 b = 180.934 β = 90 c = 183.306 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS3 S 6M 2021-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.83 48.63 100 0.131 0.142 0.055 0.997 14.2 6.6 42789
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.83 2.94 100 0.95 1.029 0.392 0.786 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.83 48.63 40666 2056 99.95 0.22953 0.22815 0.2569 0.2202 RANDOM 55.58
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] 2.36 0.53 -2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.819 r_dihedral_angle_1_deg 5.213 r_long_range_B_refined 4.325 r_long_range_B_other 4.325 r_dihedral_angle_2_deg 3.534 r_mcangle_it 2.584 r_mcangle_other 2.584 r_scangle_other 2.329 r_mcbond_it 1.473 r_mcbond_other 1.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.819 r_dihedral_angle_1_deg 5.213 r_long_range_B_refined 4.325 r_long_range_B_other 4.325 r_dihedral_angle_2_deg 3.534 r_mcangle_it 2.584 r_mcangle_other 2.584 r_scangle_other 2.329 r_mcbond_it 1.473 r_mcbond_other 1.472 r_scbond_it 1.281 r_scbond_other 1.281 r_angle_refined_deg 0.868 r_angle_other_deg 0.323 r_chiral_restr 0.041 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 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 9642 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing