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Structure of the NS5 methyltransferase from Zika bound to MS2042
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KQS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.095 M Sodium sodium citrate tribasic dihydrate, pH 5.6, 19 % v/v 2-Propanol, 19 % w/v PEG 4K, 5 % v/v glycerol
Crystal Properties Matthews coefficient Solvent content 2.83 56.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.989 α = 90 b = 111.231 β = 93.87 c = 77.4 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 S 6M 2016-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03324 APS 23-ID-D
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 1.55 50 99.9 0.063 23.1 6.3 95052
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 1.55 1.58 97.8 0.6 2.4 2.4 4622
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5KQS 1.55 35.724 1.34 95009 4620 99.71 0.1744 0.1731 0.1744 0.1992 0.2013
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.873 f_angle_d 0.845 f_chiral_restr 0.052 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3983 Nucleic Acid Atoms Solvent Atoms 601 Heterogen Atoms 110
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling Auto-Rickshaw phasing