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Crystal structure of N-methyl transferase from Plasmodium vivax complexed with S-adenosyl methionine and phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UJ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 Protein solution was at 15 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM
bME, 5 mM SAM. Mother liqueur contained 0.2 M Ammonium formate and 20% PEG 3,350. Cryoprotectant was 30% PEG 3,350 , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.96 37.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.17 α = 90 b = 86.87 β = 101.05 c = 79.58 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 2011-03-14 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 Merge 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 1.4 20 98.8 0.082 13.61 100044 98848 -3 17.259
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.44 97.4 0.556 2.99
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3UJ6 1.4 19.684 2.03 100044 98845 4943 98.87 0.166 0.1583 0.1573 0.1565 0.1785 0.1774 random 14.4367
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] -0.0568 0.0505 0.0158 0.041
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.224 f_angle_d 1.137 f_chiral_restr 0.078 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4309 Nucleic Acid Atoms Solvent Atoms 992 Heterogen Atoms 72
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection XDS data reduction