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Crystal structure of the C-terminal domain hexamer of ArgR from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B4B PDB entry 1B4B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Drops containing 1 microliter protein solution (10 mg/mL) and 0.5 microliter reservoir solution equilibrated against the reservoir solution (20% PEG 10000, 0.1 M HEPES pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.89 57.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.219 α = 66.19 b = 57.242 β = 62.21 c = 57.328 γ = 82
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 ADSC QUANTUM 315 2007-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97848 SSRL BL7-1
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 2.15 50 95 0.061 11.77 1.8 28214 28214
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 2.15 2.23 84 0.252 2.26 1.7
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 entry 1B4B 2.15 44.81 28194 26786 1406 94.94 0.1712 0.16795 0.1711 0.23464 0.1802 RANDOM 25.627
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] 0.71 -0.94 0.84 -0.55 0.37 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.762 r_dihedral_angle_3_deg 15.881 r_dihedral_angle_4_deg 14.242 r_dihedral_angle_1_deg 6.703 r_scangle_it 5.49 r_scbond_it 3.417 r_mcangle_it 1.974 r_angle_refined_deg 1.822 r_mcbond_it 1.232 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.762 r_dihedral_angle_3_deg 15.881 r_dihedral_angle_4_deg 14.242 r_dihedral_angle_1_deg 6.703 r_scangle_it 5.49 r_scbond_it 3.417 r_mcangle_it 1.974 r_angle_refined_deg 1.822 r_mcbond_it 1.232 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.249 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.169 r_symmetry_vdw_refined 0.132 r_chiral_restr 0.111 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 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 3400 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing