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Crystal structure of N-methyl transferase from Plasmodium vivax complexed with S-adenosyl methionine, phosphate and amodiaquine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UJ6 pdb entry 3UJ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 Precipitant was 20% PEG 3350, 200 mM NH4-formate; protein solution contained 10 mM EDTA, 10 mM bME, 50 mM Tris-HCl, concentration was 15 mg/mL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.98 37.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.44 α = 90 b = 86.62 β = 103.23 c = 78.27 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX-225 2012-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.5 40 99.3 0.097 9.76 153346 152303
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 98.6 0.56 2.36
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 3UJ6 1.5 36.446 1.37 77124 77118 3856 99.31 0.1763 0.153 0.1517 0.1779 0.183 random 16.1857
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 15.822 f_angle_d 1.137 f_chiral_restr 0.075 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4272 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 97
Software Software Software Name Purpose PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection XDS data reduction XSCALE data scaling