3E61

Crystal structure of a putative transcriptional repressor of ribose operon from Staphylococcus saprophyticus subsp. saprophyticus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72943M sodium formate, 275mM sodium thiocyanate, pH 7.0, Vapor diffusion, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.1843.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.146α = 90
b = 106.634β = 112.17
c = 68.183γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97958APS31-ID

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
1219.74999.70.1030.10312.35.1362253611628.1
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)
122.1199.40.5870.5872.85.15227

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 DIFFRACTIONSADTHROUGHOUT219.7493622536098184299.650.2140.2120.259RANDOM39.625
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]
-1.780.031.620.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.528
r_dihedral_angle_4_deg22.713
r_dihedral_angle_3_deg16.631
r_dihedral_angle_1_deg5.978
r_scangle_it3.925
r_scbond_it2.656
r_mcangle_it1.65
r_angle_refined_deg1.542
r_mcbond_it1.012
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.528
r_dihedral_angle_4_deg22.713
r_dihedral_angle_3_deg16.631
r_dihedral_angle_1_deg5.978
r_scangle_it3.925
r_scbond_it2.656
r_mcangle_it1.65
r_angle_refined_deg1.542
r_mcbond_it1.012
r_nbtor_refined0.312
r_symmetry_hbond_refined0.298
r_symmetry_vdw_refined0.277
r_nbd_refined0.219
r_xyhbond_nbd_refined0.144
r_chiral_restr0.111
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3691
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms12

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building