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Structure of a GNAT superfamily PA3944 acetyltransferase in complex with AcCoA
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 7 289 0.3 uL of 10 mg/mL protein incubated with 5mM AcCoA and 5 mM (R)-3-(2-chloroacetamido)-4-(((S)-1-methoxy-1-oxo-3-phenylpropan-2-yl)amino)-4-oxobutanoic acid 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).
Crystal Properties Matthews coefficient Solvent content 1.89 34.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.563 α = 97.94 b = 44.246 β = 106.72 c = 60.183 γ = 89.92
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 MARMOSAIC 300 mm CCD 2017-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
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 1.8 50 97.1 0.095 0.102 0.068 5.5 2.2 32365
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 1.8 1.83 95.6 0.592 0.809 0.549 0.553 1.9
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 1.8 37.43 28223 1392 89.22 0.2078 0.2064 0.2127 0.2354 0.2392 RANDOM 24.695
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] 5.91 1.39 3.09 -6.6 -0.33 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.819 r_dihedral_angle_4_deg 13.374 r_dihedral_angle_3_deg 12.291 r_dihedral_angle_1_deg 6.503 r_angle_refined_deg 1.18 r_angle_other_deg 1.108 r_chiral_restr 0.05 r_bond_other_d 0.004 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.819 r_dihedral_angle_4_deg 13.374 r_dihedral_angle_3_deg 12.291 r_dihedral_angle_1_deg 6.503 r_angle_refined_deg 1.18 r_angle_other_deg 1.108 r_chiral_restr 0.05 r_bond_other_d 0.004 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2975 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing Coot model building