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RNA Polymerase II Initiation Complex with a 7-nt RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NVQ PDB ENTRY 2NVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 293 390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6.000, 15mM DTT, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.69 66.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.928 α = 90 b = 220.891 β = 100.16 c = 194.623 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 2009-10-30 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 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 3.3 50 99.9 0.132 8.9 3.8 104957
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 3.3 3.42 99.9 0.761 3.7 10438
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 2NVQ 3.3 44.11 104540 5221 0.1763 0.1736 0.1907 0.2279 0.2429 RANDOM 98.2366
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] -30.645 27.0085 10.7386 19.9064
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 24.05 t_omega_torsion 2.84 t_angle_deg 1.35 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 24.05 t_omega_torsion 2.84 t_angle_deg 1.35 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28292 Nucleic Acid Atoms 414 Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose BUSTER-TNT refinement DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction BUSTER refinement