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Dengue 3 NS5 Methyltransferase bound to the substrate S-Adenosyl methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L9K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 291 22.5% Peg8000, 200mM NaCl, 20mM Na3Citrate, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.45 49.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.818 α = 90 b = 61.097 β = 90 c = 186.035 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD 2010-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 51.85 66086 62652
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 1L9K 1.7 30 66086 62652 3345 100 0.19366 0.19219 0.1912 0.22068 0.2183 RANDOM 20.32
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] 0.02 -0.72 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.212 r_dihedral_angle_1_deg 18.337 r_dihedral_angle_4_deg 15.197 r_dihedral_angle_3_deg 14.057 r_scangle_it 3.577 r_scbond_it 2.307 r_angle_refined_deg 1.643 r_mcangle_it 1.434 r_mcbond_it 0.997 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.212 r_dihedral_angle_1_deg 18.337 r_dihedral_angle_4_deg 15.197 r_dihedral_angle_3_deg 14.057 r_scangle_it 3.577 r_scbond_it 2.307 r_angle_refined_deg 1.643 r_mcangle_it 1.434 r_mcbond_it 0.997 r_nbtor_refined 0.302 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.13 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4086 Nucleic Acid Atoms Solvent Atoms 689 Heterogen Atoms 54
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling