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Crystal Structure of Dengue Methyltransferase in Complex with GpppA and S-Adenosyl-L-Homocysteine
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 2.77 55.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.722 α = 90 b = 108.722 β = 90 c = 55.921 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 2000-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.993 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 2.2 35 99.9 0.061 15.5 3.4 19634 19614 44.91
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 2.2 2.32 99.8 0.382 2.7 3.1 2825
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 (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 2.2 35 18461 18439 1157 99.88 0.19886 0.19697 0.1992 0.22761 0.2268 RANDOM 39.367
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] -0.07 -0.03 -0.07 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_dihedral_angle_4_deg 21.685 r_dihedral_angle_3_deg 18.378 r_dihedral_angle_1_deg 5.799 r_scangle_it 2.859 r_scbond_it 1.891 r_angle_refined_deg 1.476 r_mcangle_it 1.309 r_mcbond_it 0.79 r_symmetry_hbond_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_dihedral_angle_4_deg 21.685 r_dihedral_angle_3_deg 18.378 r_dihedral_angle_1_deg 5.799 r_scangle_it 2.859 r_scbond_it 1.891 r_angle_refined_deg 1.476 r_mcangle_it 1.309 r_mcbond_it 0.79 r_symmetry_hbond_refined 0.304 r_nbtor_refined 0.3 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2013 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 120
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling