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AprA Methyltransferase 1 - GNAT in complex with Mn2+ , SAM, and Di-methyl-malonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 11mg/mL protein in 50mM Tris pH7.4, 50mM NaCl, 10%(V/V) glycerol, 1mM S-adenosyl-L-homocysteine (SAH), and 5mM MnCl2.
Well solution: 15% PEG 3350, 0.1M di-methyl-malonate
Protein to well solution ratio is 2:2
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.572 α = 90 b = 88.283 β = 90 c = 135.982 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 100 PIXEL DECTRIS EIGER X 16M 2017-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.18 45.23 99.87 0.995 7.37 10.6 38749 33.02
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 2.181 2.259 99.42 0.495 1.18
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6B3A 2.18 45.23 1.35 38749 3656 99.87 0.1955 0.193 0.1932 0.2411 0.2406 40.78
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 11.8011 f_angle_d 0.8997 f_chiral_restr 0.0522 f_bond_d 0.0075 f_plane_restr 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5149 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data scaling XDS data reduction