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Crystal structure of the second DNA-Binding protein under starvation from Mycobacterium smegmatis soaked with iron in the ratio of 24 iron atoms per dodecamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6 298 100 mM sodium cacodylate, 150 mM MgCl2, 20% PEG3000
Crystal Properties Matthews coefficient Solvent content 2.32 47.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.17 α = 90 b = 90.17 β = 90 c = 420.411 γ = 120
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 2012-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.03 47.61 96.8 27.1 8.2 41744
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.14 78.2 12.4 7.2
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 2z90 2.05 30 39614 2116 98.83 0.16602 0.16424 0.165 0.19939 0.1997 RANDOM 14.656
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] 0.26 0.13 0.26 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.689 r_dihedral_angle_4_deg 17.209 r_dihedral_angle_3_deg 13.319 r_dihedral_angle_1_deg 4.935 r_long_range_B_refined 3.506 r_mcangle_it 1.17 r_angle_refined_deg 1.143 r_scbond_it 0.717 r_mcbond_it 0.666 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.689 r_dihedral_angle_4_deg 17.209 r_dihedral_angle_3_deg 13.319 r_dihedral_angle_1_deg 4.935 r_long_range_B_refined 3.506 r_mcangle_it 1.17 r_angle_refined_deg 1.143 r_scbond_it 0.717 r_mcbond_it 0.666 r_chiral_restr 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4978 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing