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x-ray structure of the psychrobacter cryohalolentis Pcryo_0637 N-acetyltransferase in the presene of its reaction tetrahedral intermediate
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
crystals incubated with 5 mM acetyl-coenzyme A and 5 mM UDP-2-acetamido-4-amino-2,4,3-trideoxy-D-glucose
Crystal Properties Matthews coefficient Solvent content 2.54 51.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.237 α = 90 b = 97.237 β = 90 c = 66.173 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 2019-04-03 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 1.399 50 98.8 0.049 20.2 5.9 45470
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 1.4 1.5 97.9 0.38 2.4 3.3
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 1.4 28.699 45470 2191 98.76 0.156 0.1552 0.1554 0.1805 0.1805 15.26
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] 0.075 0.037 0.075 -0.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.939 r_dihedral_angle_4_deg 19.346 r_dihedral_angle_3_deg 12.231 r_dihedral_angle_1_deg 7.559 r_lrange_it 5.232 r_lrange_other 5.232 r_scangle_it 3.549 r_scangle_other 3.547 r_scbond_it 2.421 r_scbond_other 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.939 r_dihedral_angle_4_deg 19.346 r_dihedral_angle_3_deg 12.231 r_dihedral_angle_1_deg 7.559 r_lrange_it 5.232 r_lrange_other 5.232 r_scangle_it 3.549 r_scangle_other 3.547 r_scbond_it 2.421 r_scbond_other 2.42 r_angle_refined_deg 2.069 r_mcangle_other 2.056 r_mcangle_it 2.043 r_angle_other_deg 1.498 r_mcbond_it 1.409 r_mcbond_other 1.352 r_symmetry_xyhbond_nbd_refined 0.212 r_xyhbond_nbd_refined 0.201 r_nbd_refined 0.199 r_symmetry_nbd_other 0.186 r_nbd_other 0.179 r_nbtor_refined 0.166 r_symmetry_nbd_refined 0.161 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1612 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing