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Crystal structure of gated-pore mutant H126/141D of second DNA-Binding protein under starvation from Mycobacterium smegmatis
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 under oil 6.5 298 50mM MgCl2, 0.1M sodium cacodylate, 20% PEG3350 , pH 6.5, Microbatch under oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.23 α = 90 b = 90.23 β = 90 c = 420.312 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 2011-07-22 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) R Merge 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 2.03 30 0.053 25.6 7 41264 13.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.14 0.139 11.7 6.4
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 Direct refinement against model PDB THROUGHOUT 2z90 2.05 30 39172 2086 98.54 0.17618 0.17463 0.1761 0.20638 0.2083 RANDOM 12.356
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] 0.32 0.16 0.32 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.168 r_dihedral_angle_4_deg 16.12 r_dihedral_angle_3_deg 13.103 r_dihedral_angle_1_deg 4.377 r_scangle_it 1.511 r_scbond_it 0.884 r_angle_refined_deg 0.855 r_mcangle_it 0.566 r_mcbond_it 0.288 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.168 r_dihedral_angle_4_deg 16.12 r_dihedral_angle_3_deg 13.103 r_dihedral_angle_1_deg 4.377 r_scangle_it 1.511 r_scbond_it 0.884 r_angle_refined_deg 0.855 r_mcangle_it 0.566 r_mcbond_it 0.288 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4929 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 8
Software Software Software Name Purpose MAR345dtb data collection REFMAC refinement MOSFLM data reduction SCALA data scaling