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AadA in complex with ATP, magnesium and streptomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 281 20% v/v PEG 500* MME; 10 % w/v PEG
20000, 0.02M DL-Glutamic acid monohydrate; 0.02M DLAlanine;
0.02M Glycine; 0.02M DL-Lysine
monohydrochloride; 0.02M DL-Serine, 0.1M Sodium HEPES-MOPS pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.67 α = 90 b = 82.67 β = 90 c = 79.86 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 173 PIXEL DECTRIS PILATUS 6M-F 2017-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07438 ESRF ID29
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 2.05 71.6 100 0.112 0.992 13.43 10.3 38252 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 99.9 1.784 0.552 1.33 10.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 5g4a 2.05 41.335 1.96 38245 1909 99.94 0.1759 0.1743 0.1759 0.2076 0.2087 Random selection 55.3
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 12.962 f_angle_d 0.66 f_chiral_restr 0.037 f_bond_d 0.013 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4141 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 168
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing