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Crystal structure of a GNAT Superfamily PA3944 acetyltransferase in complex with CoA (P1 space group)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EDV
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 CoA and 5 mM colistin 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 2.08 40.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.452 α = 81.88 b = 44.175 β = 73.32 c = 60.125 γ = 89.94
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 Beryllium Lenses 2017-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 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 1.55 50 96.2 0.053 0.069 0.044 11.7 2.4 49684
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 1.55 1.58 93.5 0.397 0.521 0.335 0.773 2.1
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 6EDV 1.55 34.89 44683 2225 91.54 0.167 0.1656 0.1772 0.1935 0.1829 RANDOM 19.859
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] 11.34 5.97 2.72 -15.22 -1.77 3.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.946 r_dihedral_angle_4_deg 16.49 r_dihedral_angle_3_deg 12.062 r_dihedral_angle_1_deg 6.522 r_angle_other_deg 1.731 r_angle_refined_deg 1.371 r_chiral_restr 0.081 r_gen_planes_other 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.946 r_dihedral_angle_4_deg 16.49 r_dihedral_angle_3_deg 12.062 r_dihedral_angle_1_deg 6.522 r_angle_other_deg 1.731 r_angle_refined_deg 1.371 r_chiral_restr 0.081 r_gen_planes_other 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3036 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 130
Software Software Software Name Purpose HKL-3000 data reduction HKL-3000 data scaling SCALEPACK data scaling HKL-3000 phasing MOLREP phasing Coot model building REFMAC refinement