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Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D3B PDB ID 3D3B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 293 0.1 M Tris-HCl, pH 7.1, 0.2 M ammonium sulfate, 25 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113 α = 90 b = 113 β = 90 c = 267.2 γ = 90
Symmetry Space Group I 41 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 100 PIXEL PILATUS 6M mirrors 2007-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9763 SLS X10SA
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 2.3 30 100 0.141 0.141 16.2 12.7 39315 26358
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 100 0.314 0.314 8.3 12.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 ID 3D3B 2.6 30 38823 25020 1317 100 0.22078 0.21766 0.2806 0.27988 0.3183 RANDOM 44.323
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] -0.47 -0.47 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.774 r_dihedral_angle_3_deg 18.177 r_dihedral_angle_4_deg 16.478 r_dihedral_angle_1_deg 5.4 r_angle_refined_deg 1.09 r_scangle_it 0.8 r_mcangle_it 0.513 r_scbond_it 0.449 r_symmetry_vdw_refined 0.343 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.774 r_dihedral_angle_3_deg 18.177 r_dihedral_angle_4_deg 16.478 r_dihedral_angle_1_deg 5.4 r_angle_refined_deg 1.09 r_scangle_it 0.8 r_mcangle_it 0.513 r_scbond_it 0.449 r_symmetry_vdw_refined 0.343 r_nbtor_refined 0.295 r_mcbond_it 0.284 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_refined 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 5308 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XDS data scaling MOLREP phasing