5WW3

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z90 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6298100 mM sodium cacodylate, 150 mM MgCl2, 20% PEG3000
Crystal Properties
Matthews coefficientSolvent content
2.3247.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.17α = 90
b = 90.17β = 90
c = 420.411γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2012-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54179

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0347.6196.827.18.241744
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.032.1478.212.47.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2z902.053039614211698.830.166020.164240.19939RANDOM14.656
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]
0.260.130.26-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.689
r_dihedral_angle_4_deg17.209
r_dihedral_angle_3_deg13.319
r_dihedral_angle_1_deg4.935
r_long_range_B_refined3.506
r_mcangle_it1.17
r_angle_refined_deg1.143
r_scbond_it0.717
r_mcbond_it0.666
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.689
r_dihedral_angle_4_deg17.209
r_dihedral_angle_3_deg13.319
r_dihedral_angle_1_deg4.935
r_long_range_B_refined3.506
r_mcangle_it1.17
r_angle_refined_deg1.143
r_scbond_it0.717
r_mcbond_it0.666
r_chiral_restr0.087
r_bond_refined_d0.008
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms4978
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing