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Crystal structure of streptogramin A acetyltransferase VatA from Staphylococcus aureus in complex with streptogramin analog F1037 (47)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HUR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M (NH4)2SO4, 0.1 M phosphate-citrate pH 4.2, 20 %v/v PEG 300; 10 % glycerol
Crystal Properties Matthews coefficient Solvent content 3.31 62.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.54 α = 90 b = 105.62 β = 90 c = 178.2 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 92 PIXEL DECTRIS PILATUS3 6M 2019-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11583 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 3.05 89.138 99.92 0.3773 0.989 6.67 13.2 38654 65.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.159 99.92 0.575 12.8
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4HUR 3.05 89.138 38637 99.92 0.2335 0.2311 0.2662 0.2617 64.13
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.6739 f_angle_d 1.1023 f_chiral_restr 0.0652 f_bond_d 0.0091 f_plane_restr 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10207 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement PHENIX phasing xia2 data reduction xia2 data scaling