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Crystal Structure of an RNA polymerase II-TFIIB complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R5U 1R5U WITHOUT CHAIN M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 295 1.2 M sodium/potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.57 73.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.15 α = 90 b = 216.21 β = 90 c = 420.98 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 325 mm CCD 2008-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.8 210.49 98.6 0.093 0.093 9.6 3.9 89990
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.8 4.01 99.3 0.545 0.545 0.75 0.37 1.3 3.9 13147
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 1R5U WITHOUT CHAIN M 3.8 50 87509 4320 95.51 0.268 0.263 0.261 0.313 0.3115 RANDOM 188.144
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] 57.328 -22.441 -34.888
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 49.942 r_dihedral_angle_2_deg 42.006 r_mcbond_it 36.389 r_scangle_it 30.115 r_scbond_it 22.238 r_dihedral_angle_3_deg 17.839 r_dihedral_angle_4_deg 17.78 r_dihedral_angle_1_deg 5.222 r_angle_refined_deg 1.363 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 49.942 r_dihedral_angle_2_deg 42.006 r_mcbond_it 36.389 r_scangle_it 30.115 r_scbond_it 22.238 r_dihedral_angle_3_deg 17.839 r_dihedral_angle_4_deg 17.78 r_dihedral_angle_1_deg 5.222 r_angle_refined_deg 1.363 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29020 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 9
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CNS refinement