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Crystal Structure of Dengue Methyltransferase in Complex with GpppG 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 2.95 58.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.502 α = 90 b = 111.502 β = 90 c = 56.534 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 2003-02-01 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 2.75 35 99.9 0.056 21.7 5.1 10793 10782 97.65
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 2.75 2.9 99.7 0.508 2.7 4.8 1551
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 2.75 32.21 10128 10118 656 99.9 0.21173 0.21173 0.20792 0.2073 0.27069 0.2641 RANDOM 77.147
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] 0.34 0.17 0.34 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.274 r_dihedral_angle_4_deg 19.232 r_dihedral_angle_3_deg 19.162 r_dihedral_angle_1_deg 7.293 r_scangle_it 3.503 r_scbond_it 2.441 r_angle_refined_deg 1.779 r_mcangle_it 1.535 r_mcbond_it 1.19 r_symmetry_hbond_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.274 r_dihedral_angle_4_deg 19.232 r_dihedral_angle_3_deg 19.162 r_dihedral_angle_1_deg 7.293 r_scangle_it 3.503 r_scbond_it 2.441 r_angle_refined_deg 1.779 r_mcangle_it 1.535 r_mcbond_it 1.19 r_symmetry_hbond_refined 0.316 r_nbtor_refined 0.314 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.215 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2022 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 80
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling