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The closed ring structure of the Rho transcription termination factor in complex with nucleic acid in the motor domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PVO PDB ENTRY 1PVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch under paraffine oil 6.5 291 50 mM Na cacodylate, 10 mM MgOAc, 1.8 M LiSO4, 2%
benzamidine, 10 mM spermine-HCl, pH 6.5, Microbatch under paraffine oil, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.87 68.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 257.686 α = 90 b = 257.686 β = 90 c = 257.686 γ = 90
Symmetry Space Group I 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
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 3.5 20 92 15818 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.68 86.9
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 (All) 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 1PVO 3.51 20 1.7 15818 854 91.9 0.2857 0.28707 0.29446 0.2752 0.3281 0.3245 RANDOM 118.555
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 r_dihedral_angle_2_deg 36.54 r_dihedral_angle_3_deg 17.819 r_dihedral_angle_4_deg 13.812 r_dihedral_angle_1_deg 4.85 r_angle_refined_deg 0.95 r_nbtor_refined 0.3 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.54 r_dihedral_angle_3_deg 17.819 r_dihedral_angle_4_deg 13.812 r_dihedral_angle_1_deg 4.85 r_angle_refined_deg 0.95 r_nbtor_refined 0.3 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.093 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5042 Nucleic Acid Atoms 171 Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling