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RNA polymerase II elongation complex B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R9T pdb entry 1R9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 390mM (NH4)2HPO4/NaH2PO4, 50mM dioxane, 10mM DTT, 9-11% PEG6,000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.62 66.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.114 α = 90 b = 222.131 β = 100.99 c = 191.782 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 77 CCD MARMOSAIC 325 mm CCD 2008-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979 SSRL BL11-1
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 3.57 40 92.3 0.166 6.3 2.5 74144 70340
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) 3.57 3.66 92.7 0.716 1.4 2.3
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 pdb entry 1R9T 3.57 40 70340 3681 90.5 0.24391 0.24138 0.2483 0.29233 0.292 RANDOM 130.199
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] 1.69 -2.21 -1.65 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.565 r_dihedral_angle_3_deg 23.706 r_dihedral_angle_4_deg 20.522 r_dihedral_angle_1_deg 7.611 r_scangle_it 1.899 r_angle_refined_deg 1.568 r_mcangle_it 1.116 r_scbond_it 1.054 r_mcbond_it 0.613 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.565 r_dihedral_angle_3_deg 23.706 r_dihedral_angle_4_deg 20.522 r_dihedral_angle_1_deg 7.611 r_scangle_it 1.899 r_angle_refined_deg 1.568 r_mcangle_it 1.116 r_scbond_it 1.054 r_mcbond_it 0.613 r_chiral_restr 0.105 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28140 Nucleic Acid Atoms 1069 Solvent Atoms Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data collection MLPHARE phasing REFMAC refinement DENZO data reduction HKL-2000 data scaling