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x-ray structure of the N-acetyltransferase Pcryo_0637 from psychrobacter cryohalolentis in the presence of UDP and acetyl-conezyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M9C
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 acetyl-coenzyme A and 5 mM UDP
Crystal Properties Matthews coefficient Solvent content 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.656 α = 90 b = 97.656 β = 90 c = 65.525 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 2019-04-25 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 98.2 0.062 17.6 6.1 56307
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 96.6 0.436 3 2.8
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 MOLECULAR REPLACEMENT FREE R-VALUE 4m9c 1.3 28.746 56307 2917 98.248 0.195 0.1938 0.203 0.2136 0.2222 12.367
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] -0.091 -0.045 -0.091 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.265 r_dihedral_angle_4_deg 21.798 r_dihedral_angle_3_deg 12.013 r_dihedral_angle_1_deg 7.635 r_lrange_it 4.955 r_lrange_other 4.59 r_scangle_it 3.345 r_scangle_other 3.343 r_scbond_it 2.24 r_scbond_other 2.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.265 r_dihedral_angle_4_deg 21.798 r_dihedral_angle_3_deg 12.013 r_dihedral_angle_1_deg 7.635 r_lrange_it 4.955 r_lrange_other 4.59 r_scangle_it 3.345 r_scangle_other 3.343 r_scbond_it 2.24 r_scbond_other 2.239 r_mcangle_it 1.881 r_mcangle_other 1.881 r_angle_refined_deg 1.873 r_angle_other_deg 1.453 r_mcbond_it 1.255 r_mcbond_other 1.254 r_xyhbond_nbd_refined 0.238 r_nbd_refined 0.201 r_nbd_other 0.198 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.153 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1617 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing