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Dengue serotype 3 RNA-dependent RNA polymerase bound to PC-79-SH52
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HHJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 0.1M TRIS PH 8.0, 25% PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 2.79 55.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.3 α = 90 b = 176.22 β = 90 c = 57.84 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 PIXEL DECTRIS PILATUS 2M 2013-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2 118.982 98.7 0.095 0.105 0.043 10.7 5.3 55382 55382 31.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.071 94.9 0.4321 0.695 0.372 1.79 4 7747
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 4HHJ 2 29.28 55362 2813 98.61 0.1856 0.1838 0.1904 0.2191 0.2285 RANDOM 41.13
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] 6.7399 -15.4525 8.7126
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.99 t_omega_torsion 3.14 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.99 t_omega_torsion 3.14 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4762 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 19
Software Software Software Name Purpose SCALA data scaling BUSTER-TNT refinement PDB_EXTRACT data extraction SCALA data scaling BUSTER-TNT phasing