3KEO

Crystal Structure of a Rex-family transcriptional regulatory protein from Streptococcus agalactiae complexed with NAD+


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729320% PEG 6000, 175mM magnesium chloride, 100mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1141.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.27α = 90
b = 92.41β = 91.26
c = 47.19γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2009-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.0379MAX III911-2

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
11.527.1980.0848.423.66336062064-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.5493.30.5282.263.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2DT51.527.0758774314797.620.178450.175440.23436RANDOM11.49
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]
-0.050.040.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.295
r_dihedral_angle_4_deg21.74
r_dihedral_angle_3_deg13.137
r_sphericity_free10.687
r_scangle_it6.375
r_dihedral_angle_1_deg5.406
r_scbond_it4.639
r_sphericity_bonded4.262
r_mcangle_it3.176
r_rigid_bond_restr2.268
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.295
r_dihedral_angle_4_deg21.74
r_dihedral_angle_3_deg13.137
r_sphericity_free10.687
r_scangle_it6.375
r_dihedral_angle_1_deg5.406
r_scbond_it4.639
r_sphericity_bonded4.262
r_mcangle_it3.176
r_rigid_bond_restr2.268
r_mcbond_it2.19
r_angle_refined_deg2.038
r_angle_other_deg1.101
r_mcbond_other0.944
r_chiral_restr0.137
r_bond_refined_d0.025
r_gen_planes_refined0.01
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3258
Nucleic Acid Atoms
Solvent Atoms544
Heterogen Atoms96

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling