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crystal structure of the Pcryo_0619 N-acetyltransferase from Psychrobacter cryohalolentis K5 int he presence of acetyl coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 Protein incubated with 3 mM acetyl-CoA. Precipitant: 8-12% PEG 8000 and 100 mM homopipes (pH 5)
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.895 α = 90 b = 157.818 β = 90 c = 66.046 γ = 90
Symmetry Space Group P 21 21 2
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 2019-11-19 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 1.9 50 99.7 0.084 14.3 11.5 89307
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 1.9 2 99.2 0.4 2.8 5.5
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 1.9 29.69 84841 4466 99.7 0.19948 0.19733 0.2035 0.23993 0.2444 RANDOM 18.034
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.192 r_dihedral_angle_2_deg 11.503 r_dihedral_angle_1_deg 6.671 r_long_range_B_refined 5.259 r_long_range_B_other 5.259 r_scangle_other 3.797 r_mcangle_it 2.358 r_mcangle_other 2.358 r_scbond_it 2.338 r_scbond_other 2.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.192 r_dihedral_angle_2_deg 11.503 r_dihedral_angle_1_deg 6.671 r_long_range_B_refined 5.259 r_long_range_B_other 5.259 r_scangle_other 3.797 r_mcangle_it 2.358 r_mcangle_other 2.358 r_scbond_it 2.338 r_scbond_other 2.338 r_mcbond_it 1.471 r_mcbond_other 1.469 r_angle_refined_deg 1.366 r_angle_other_deg 0.449 r_chiral_restr 0.06 r_gen_planes_refined 0.007 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 8064 Nucleic Acid Atoms Solvent Atoms 672 Heterogen Atoms 355
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing