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Structure of a GNAT superfamily PA3944 acetyltransferase in complex with zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EDD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.3 uL of 8 mg/mL protein incubated with 2.5 mM CoA was mixed with 0.2 uL of the well condition (MCSG suite I condition 11 - 100 mM Tris-HCl pH 7.0, 200 mM calcium acetate, 20% w/v PEG 3000) and equilibrated against well solution in 96 Well 3 drop Crystallization Plate (Swissci). The obtained crystals were soaked with 10 mM (R)-3-(2-chloroacetamido)-4-(((S)-1-methoxy-1-oxo-3-phenylpropan-2-yl)amino)-4-oxobutanoic acid.
Crystal Properties Matthews coefficient Solvent content 2.05 39.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.423 α = 98.05 b = 43.801 β = 109.51 c = 60.793 γ = 90.1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2016-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.979 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 97.4 0.107 0.151 0.107 10.6 1.9 22739
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 2.03 95.8 0.455 0.644 0.455 0.379 1.8
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 (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 6EDD 2 32.17 19513 1070 87.07 0.2021 0.1998 0.2046 0.2452 0.2486 RANDOM 31.369
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] -10.94 -3.53 -4.78 0.03 2.15 10.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.559 r_dihedral_angle_4_deg 12.918 r_dihedral_angle_3_deg 12.76 r_dihedral_angle_1_deg 6.531 r_angle_other_deg 1.49 r_angle_refined_deg 1.248 r_chiral_restr 0.06 r_bond_other_d 0.018 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.559 r_dihedral_angle_4_deg 12.918 r_dihedral_angle_3_deg 12.76 r_dihedral_angle_1_deg 6.531 r_angle_other_deg 1.49 r_angle_refined_deg 1.248 r_chiral_restr 0.06 r_bond_other_d 0.018 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3025 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 112
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing Coot model building