☰ Navigation Tabs
Crystal Structure of Dengue Methyltransferase in Complex with 7MeGpppA 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 2.94 58.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.56 α = 90 b = 111.56 β = 90 c = 56.33 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 2.756 27.96 97.1 0.083 27.4 5.2 10324 10025
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 2.756 2.95 97.1 0.515 3.4 5.1 1448
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1L9K 2.756 27.96 9592 9409 609 98.09 0.19783 0.19466 0.24372 0.2311 RANDOM 65.565
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] -2.2 -1.1 -2.2 3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.239 r_dihedral_angle_4_deg 22.944 r_dihedral_angle_3_deg 18.451 r_dihedral_angle_1_deg 6.426 r_scangle_it 2.814 r_scbond_it 1.67 r_angle_refined_deg 1.615 r_mcangle_it 1.161 r_mcbond_it 0.685 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.239 r_dihedral_angle_4_deg 22.944 r_dihedral_angle_3_deg 18.451 r_dihedral_angle_1_deg 6.426 r_scangle_it 2.814 r_scbond_it 1.67 r_angle_refined_deg 1.615 r_mcangle_it 1.161 r_mcbond_it 0.685 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.281 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.203 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2022 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 135
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling