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Crystal Structure of Dengue Methyltransferase in Complex with 7MeGpppG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L9K PDB ENTRY 1L9K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 293 0.4 M Ammonium Sulfate, 0.1 M Sodium Citrate, 1.2 M Lithium Sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.12 60.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.725 α = 90 b = 114.725 β = 90 c = 56.426 γ = 120
Symmetry Space Group P 31 2 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 2004-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 2.7 35 99.9 0.088 21.7 8.2 12041 12029 63.8
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 2.7 2.85 100 0.33 5.1 8.3 1750
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB ENTRY 1L9K 2.701 31.27 11291 11291 720 100 0.20674 0.20674 0.20361 0.2038 0.25468 0.2513 RANDOM 46.159
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] 1.83 0.91 1.83 -2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_3_deg 19.276 r_dihedral_angle_4_deg 14.618 r_dihedral_angle_1_deg 6.602 r_scangle_it 2.272 r_angle_refined_deg 1.433 r_scbond_it 1.285 r_mcangle_it 1.138 r_mcbond_it 0.641 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_3_deg 19.276 r_dihedral_angle_4_deg 14.618 r_dihedral_angle_1_deg 6.602 r_scangle_it 2.272 r_angle_refined_deg 1.433 r_scbond_it 1.285 r_mcangle_it 1.138 r_mcbond_it 0.641 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.265 r_symmetry_hbond_refined 0.23 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.1 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2061 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 107
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling