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Crystal Structure of the Second Dps from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch method under oil 6.5 293 20mM Tris-HCl (pH 7.9), 200 mM NaCl, PEG-3000, 200mM MgCl2, 0.1M sodium cacodylate (pH 6.5), Microbatch method under oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.008 α = 90 b = 90.008 β = 90 c = 421.522 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 mirrors 2006-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 30 99.9 0.143 15.3 17.2 26434 30.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 99.3 0.48 3.5 2584
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 1O9R 2.4 29.94 26434 1276 99.8 0.187 0.187 0.1924 0.227 0.2309 RANDOM 27.8
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] 3.13 2.55 3.13 -6.25
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.2 c_scangle_it 2.63 c_scbond_it 1.91 c_mcangle_it 1.76 c_angle_deg 1.2 c_mcbond_it 1.15 c_improper_angle_d 0.88 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.2 c_scangle_it 2.63 c_scbond_it 1.91 c_mcangle_it 1.76 c_angle_deg 1.2 c_mcbond_it 1.15 c_improper_angle_d 0.88 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4973 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 8
Software Software Software Name Purpose CNS refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing