5TJJ

Crystal structure of IcIR transcriptional regulator from Alicyclobacillus acidocaldarius


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72770.8 M succinic acid, pH 7.0, cryo 30% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.550.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.38α = 90
b = 98.38β = 90
c = 119.485γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2011-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97926APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.53099.80.12212.564.720970-3
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)
12.52.541000.90.6321.994.8

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 DIFFRACTIONSADTHROUGHOUT2.53019818105199.760.191980.189670.23426RANDOM50.146
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]
-0.61-0.611.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.185
r_dihedral_angle_4_deg17.73
r_dihedral_angle_3_deg13.82
r_dihedral_angle_1_deg5.651
r_long_range_B_refined3.532
r_long_range_B_other3.532
r_scangle_other2.6
r_mcangle_it1.921
r_mcangle_other1.92
r_scbond_it1.616
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.185
r_dihedral_angle_4_deg17.73
r_dihedral_angle_3_deg13.82
r_dihedral_angle_1_deg5.651
r_long_range_B_refined3.532
r_long_range_B_other3.532
r_scangle_other2.6
r_mcangle_it1.921
r_mcangle_other1.92
r_scbond_it1.616
r_scbond_other1.615
r_angle_refined_deg1.479
r_mcbond_it1.165
r_mcbond_other1.164
r_angle_other_deg0.962
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms3949
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
BUCCANEERmodel building