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Crystal structure of the "-35 element" promoter recognition domain of Mycobacterium tuberculosis SigC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OR7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 1.8M ammonium sulphate, 0.1M MES (pH 6.5), 1mM DTT, 5% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.95 68.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.33 α = 90 b = 161.33 β = 90 c = 161.33 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2005-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 40.29 99.4 0.105 11.1 3.4 7040 1
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) 1 3 3.16 0.546 2 2.9 1002
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 1OR7 3 37.01 6707 331 99.31 0.21628 0.21359 0.2238 0.27131 0.2648 RANDOM 47.157
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 30.127 r_dihedral_angle_1_deg 23.611 r_dihedral_angle_3_deg 22.484 r_dihedral_angle_4_deg 18.169 r_scangle_it 3.244 r_angle_refined_deg 2.235 r_scbond_it 1.87 r_mcangle_it 1.128 r_mcbond_it 0.616 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.127 r_dihedral_angle_1_deg 23.611 r_dihedral_angle_3_deg 22.484 r_dihedral_angle_4_deg 18.169 r_scangle_it 3.244 r_angle_refined_deg 2.235 r_scbond_it 1.87 r_mcangle_it 1.128 r_mcbond_it 0.616 r_nbtor_refined 0.327 r_nbd_refined 0.293 r_symmetry_vdw_refined 0.236 r_xyhbond_nbd_refined 0.208 r_chiral_restr 0.164 r_bond_refined_d 0.016 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_refined r_metal_ion_other 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 1346 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing