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Crystal structure of the C-terminal domain hexamer of ArgR from Mycobacterium tuberculosis in complex with arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B4B PDB entry 1B4B, poly-alanine model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 20% PEG 10000, 0.1 M Tris-HCl, 0.1 M Guanidine-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.35 47.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.673 α = 90 b = 75.947 β = 90 c = 107.099 γ = 90
Symmetry Space Group P 21 21 21
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 225 mm CCD 2007-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97947 SSRL BL7-1
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 1.85 61.9 99.8 0.094 0.094 17.79 4.8 41086 41086 29.3
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 1.85 1.92 99.2 0.8 0.8 2.03 4.5
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 entry 1B4B, poly-alanine model 1.85 43.77 39073 38983 2028 99.77 0.17928 0.17686 0.1776 0.22538 0.1773 RANDOM 22.233
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] -1.65 2.05 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.697 r_dihedral_angle_4_deg 16.297 r_dihedral_angle_3_deg 14.569 r_dihedral_angle_1_deg 6.072 r_scangle_it 4.097 r_scbond_it 2.615 r_angle_refined_deg 1.57 r_mcangle_it 1.372 r_mcbond_it 0.946 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.697 r_dihedral_angle_4_deg 16.297 r_dihedral_angle_3_deg 14.569 r_dihedral_angle_1_deg 6.072 r_scangle_it 4.097 r_scbond_it 2.615 r_angle_refined_deg 1.57 r_mcangle_it 1.372 r_mcbond_it 0.946 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.098 r_bond_refined_d 0.015 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_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 3385 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing