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x-ray structure of the N-acetyltransferase Pcryo_0637 from psychrobacter cryohalolentis in the presence of coenzyme A and UDP-di-N-acetyl-bacillosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L7Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 23-26% MPD, 100 mM HEPES.
protein incubated with 5 mM coenzyme A and 20 mM UDP-2,4-diacetamido-2,4,6-trideoxy-D-glucose
Crystal Properties Matthews coefficient Solvent content 2.54 51.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.898 α = 90 b = 96.898 β = 90 c = 66.63 γ = 120
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 2019-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54718
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 1.55 50 98.1 0.045 19.6 5.1 33312
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 1.55 1.65 95 0.341 3 2.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 7l7y 1.55 30.983 33312 1712 98.124 0.164 0.162 0.1722 0.1903 0.1978 18.657
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] 0.228 0.114 0.228 -0.739
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.108 r_dihedral_angle_4_deg 20.082 r_dihedral_angle_3_deg 12.744 r_dihedral_angle_1_deg 7.971 r_lrange_other 5.323 r_lrange_it 5.321 r_scangle_it 3.971 r_scangle_other 3.97 r_scbond_it 2.803 r_scbond_other 2.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.108 r_dihedral_angle_4_deg 20.082 r_dihedral_angle_3_deg 12.744 r_dihedral_angle_1_deg 7.971 r_lrange_other 5.323 r_lrange_it 5.321 r_scangle_it 3.971 r_scangle_other 3.97 r_scbond_it 2.803 r_scbond_other 2.802 r_mcangle_other 2.318 r_mcangle_it 2.316 r_mcbond_it 1.662 r_mcbond_other 1.653 r_angle_refined_deg 1.634 r_angle_other_deg 1.367 r_nbd_other 0.312 r_symmetry_nbd_refined 0.301 r_symmetry_xyhbond_nbd_refined 0.261 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.161 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.066 r_xyhbond_nbd_other 0.03 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1612 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing