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Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7SK RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 277 crystallization solution 0.2M Lithium sulfate, 0.1M phosphate/citrate, pH 4.2, 25% w/v PEG mixed 1:2 volume ratio to 10 mg/mL protein:RNA complex. Crystals were soaked in crystallization solution supplemented with 1.2mM MgCl2 for 2hrs prior to freezing.
Crystal Properties Matthews coefficient Solvent content 3.61 65.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.69 α = 90 b = 119.69 β = 90 c = 77.82 γ = 120
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 6M-F 2018-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.1 51.827 99.8 0.056 0.062 0.999 15.61 5.132 37061 44.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 99.8 0.78 0.87 0.711 1.9 5.196
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 THROUGHOUT 5UNA 2.1 51.827 1.34 37052 3706 99.83 0.1772 0.1748 0.1783 0.1988 0.2012 54.1953
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 14.077 f_angle_d 0.994 f_chiral_restr 0.048 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1759 Nucleic Acid Atoms 776 Solvent Atoms 91 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction