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Crystal structure of 5-Carboxycytosine Recognition by RNA Polymerase II during Transcription Elongation.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293.15 390 mM (NH4)2HPO4/NaH2PO4, 50 mM dioxane, 10 mM DTT, and 10.7-11.6%(w/v) PEG6000
Crystal Properties Matthews coefficient Solvent content 3.66 66.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.703 α = 90 b = 221.644 β = 100.35 c = 192.41 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 3x3 CCD array (ADSC Q315R) 2012-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 3.5 50 94.3 0.143 5.1 3.6 81682 75.69
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 3.5 3.56 72.8 0.583 3.3 3157
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 3M3Y 3.5 49.273 1.34 81638 4088 94.11 0.2027 0.2011 0.2011 0.2324 0.2325 94.31
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 20.494 f_angle_d 1.355 f_chiral_restr 0.084 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28089 Nucleic Acid Atoms 1069 Solvent Atoms Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building REFMAC refinement