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Crystal structure of the oligomerization domain hexamer of the arginine repressor protein from Mycobacterium tuberculosis in complex with 9 arginines.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZFZ PDB entry 2ZFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 12% PEG 10000, 0.1M Hepes pH 7.0, 0.2M L-arginine, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.34 47.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.745 α = 90 b = 75.648 β = 90 c = 108.022 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 BL9-2 1.10552 SSRL BL9-2
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 1.9 50 95.6 0.132 0.132 15.7 6.9 36125 36125
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 1.9 1.97 84.6 0.422 0.422 4.2 6.8 3141
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 PDB entry 2ZFZ 1.9 42.26 34288 1793 95.37 0.17083 0.16813 0.1701 0.22414 0.1706 RANDOM 23.608
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] -0.7 1.78 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.849 r_dihedral_angle_3_deg 15.528 r_dihedral_angle_4_deg 15.397 r_dihedral_angle_1_deg 5.776 r_scangle_it 4.057 r_scbond_it 2.616 r_angle_refined_deg 1.483 r_mcangle_it 1.432 r_mcbond_it 0.96 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.849 r_dihedral_angle_3_deg 15.528 r_dihedral_angle_4_deg 15.397 r_dihedral_angle_1_deg 5.776 r_scangle_it 4.057 r_scbond_it 2.616 r_angle_refined_deg 1.483 r_mcangle_it 1.432 r_mcbond_it 0.96 r_nbtor_refined 0.301 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.153 r_symmetry_vdw_refined 0.146 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3393 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing