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Backtracked RNA polymerase II complex with 12mer RNA
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, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.74 67.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.956 α = 90 b = 223.004 β = 102.28 c = 195.412 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 MARMOSAIC 325 mm CCD 2007-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.78 50 96.3 8.6 3 67914
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.78 3.94 94.4 1.7 2.7
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 3.78 50 64473 3441 95.39 0.25497 0.25259 0.2539 0.29986 0.2924 RANDOM 143.007
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] 3.87 -9.5 -6.04 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.393 r_dihedral_angle_3_deg 22.858 r_dihedral_angle_4_deg 19.468 r_dihedral_angle_1_deg 8.463 r_mcangle_it 4.287 r_scangle_it 3.018 r_mcbond_it 2.408 r_scbond_it 1.63 r_angle_refined_deg 1.593 r_symmetry_vdw_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.393 r_dihedral_angle_3_deg 22.858 r_dihedral_angle_4_deg 19.468 r_dihedral_angle_1_deg 8.463 r_mcangle_it 4.287 r_scangle_it 3.018 r_mcbond_it 2.408 r_scbond_it 1.63 r_angle_refined_deg 1.593 r_symmetry_vdw_refined 0.32 r_nbtor_refined 0.318 r_nbd_refined 0.28 r_symmetry_hbond_refined 0.28 r_metal_ion_refined 0.21 r_xyhbond_nbd_refined 0.195 r_chiral_restr 0.111 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 28948 Nucleic Acid Atoms 1110 Solvent Atoms 1 Heterogen Atoms 9
Software Software Software Name Purpose MAR345 data collection REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling