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Dengue virus NS5 RNA dependent RNA polymerase domain complexed with 3' dGTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J7U PDB ENTRY 2J7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1 M TRIS HCL AT PH 8.5, 0.8M K/NA TARTRATE, 0.5% W/V PEG MME 5K
Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.716 α = 90 b = 180.918 β = 90 c = 58.042 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH MIRRORS 2006-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 48 99.6 0.01 13.98 4.9 26929
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.71 100 0.63 2.54 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2J7U 2.6 20 25549 1340 99.7 0.217 0.213 0.2072 0.289 0.2798 RANDOM 62.4
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] -0.3 1.75 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.795 r_dihedral_angle_3_deg 17.058 r_dihedral_angle_4_deg 13.008 r_dihedral_angle_1_deg 5.45 r_scangle_it 1.843 r_angle_refined_deg 1.158 r_scbond_it 1.115 r_mcangle_it 0.813 r_mcbond_it 0.46 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.795 r_dihedral_angle_3_deg 17.058 r_dihedral_angle_4_deg 13.008 r_dihedral_angle_1_deg 5.45 r_scangle_it 1.843 r_angle_refined_deg 1.158 r_scbond_it 1.115 r_mcangle_it 0.813 r_mcbond_it 0.46 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4621 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling AMoRE phasing