5N1C

Iodinated form of the Mycobacterium tuberculosis repressor EthR2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.2293200 mM NaCl, 200 mM Na citrate pH 4.2 and 15% polyethylene glycol monomethylether 5000
Crystal Properties
Matthews coefficientSolvent content
1.9938.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.43α = 90
b = 75.04β = 90
c = 88γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2013-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-D1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.66099.60.2340.99919.338.51252049.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6798.91.70.72.626.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.657.11187862699.160.243250.239970.30802RANDOM48.089
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]
-0.050.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.928
r_dihedral_angle_3_deg15.782
r_dihedral_angle_4_deg13.045
r_long_range_B_refined9.451
r_long_range_B_other9.45
r_dihedral_angle_1_deg6.458
r_scangle_other6.186
r_mcangle_it5.227
r_mcangle_other5.226
r_scbond_it4.047
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.928
r_dihedral_angle_3_deg15.782
r_dihedral_angle_4_deg13.045
r_long_range_B_refined9.451
r_long_range_B_other9.45
r_dihedral_angle_1_deg6.458
r_scangle_other6.186
r_mcangle_it5.227
r_mcangle_other5.226
r_scbond_it4.047
r_scbond_other4.046
r_mcbond_it3.353
r_mcbond_other3.353
r_angle_refined_deg1.553
r_angle_other_deg0.976
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2911
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
PHASERphasing
PARROTphasing
BUCCANEERmodel building