3CDH

Crystal structure of the MarR family transcriptional regulator SPO1453 from Silicibacter pomeroyi DSS-3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52892.0M Ammonium sulfate, 0.1M Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
4.4272.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.14α = 90
b = 124.14β = 90
c = 140.186γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPS-1Mirrors2007-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9793APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.6935.3799.50.1150.1157.211.91803618036-355.32
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.692.894.20.8350.8352.612.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.6935.37179601796091598.420.201540.200190.22748RANDOM54.7
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]
-0.69-0.34-0.691.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.829
r_dihedral_angle_3_deg21.75
r_dihedral_angle_4_deg20.544
r_scangle_it5.421
r_dihedral_angle_1_deg5.213
r_mcangle_it3.919
r_scbond_it3.281
r_mcbond_it2.268
r_angle_refined_deg1.623
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.829
r_dihedral_angle_3_deg21.75
r_dihedral_angle_4_deg20.544
r_scangle_it5.421
r_dihedral_angle_1_deg5.213
r_mcangle_it3.919
r_scbond_it3.281
r_mcbond_it2.268
r_angle_refined_deg1.623
r_nbtor_refined0.311
r_symmetry_hbond_refined0.31
r_symmetry_vdw_refined0.26
r_nbd_refined0.253
r_xyhbond_nbd_refined0.18
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2093
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms48

Software

Software
Software NamePurpose
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMACrefinement
SBC-Collectdata collection
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing