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Crystal structure of gated-pore mutant D138H 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 100mM MgCl2, 0.1M sodium cacodylate, 20% PEG3350, pH 6.5, Microbatch under oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.49 α = 90 b = 89.49 β = 90 c = 420.4 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 2011-07-23 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 0.042 37 8.8 41333 11.2
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 0.101 18.5 8.3
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 39234 2092 99.07 0.16871 0.16675 0.1686 0.20654 0.2098 RANDOM 10.167
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] 0.25 0.13 0.25 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.977 r_dihedral_angle_4_deg 14.906 r_dihedral_angle_3_deg 12.5 r_dihedral_angle_1_deg 4.333 r_scangle_it 1.488 r_scbond_it 0.871 r_angle_refined_deg 0.838 r_mcangle_it 0.551 r_mcbond_it 0.281 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.977 r_dihedral_angle_4_deg 14.906 r_dihedral_angle_3_deg 12.5 r_dihedral_angle_1_deg 4.333 r_scangle_it 1.488 r_scbond_it 0.871 r_angle_refined_deg 0.838 r_mcangle_it 0.551 r_mcbond_it 0.281 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4888 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 12
Software Software Software Name Purpose MAR345dtb data collection REFMAC refinement MOSFLM data reduction SCALA data scaling