2HWV

Crystal structure of an essential response regulator DNA binding domain, VicRc in Enterococcus faecalis, a member of the YycF subfamily.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52911.8M ammonium sulphate, 0.1M sodium citrate, 3% dimethyl sulfoxide, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.7128.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.235α = 90
b = 36.235β = 90
c = 73.935γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOsmic Confocal Max-Flux2006-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

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
11.936.22699.50.0530.05311.26.27524752427.3
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)
11.9298.90.3470.3474.85.71083

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ1.9127545713434599.570.181140.178650.23619RANDOM19.596
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]
0.770.77-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.973
r_dihedral_angle_4_deg19.526
r_dihedral_angle_3_deg18.347
r_dihedral_angle_1_deg6.899
r_scangle_it3.674
r_scbond_it2.36
r_angle_refined_deg1.497
r_mcangle_it1.407
r_mcbond_it0.864
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.973
r_dihedral_angle_4_deg19.526
r_dihedral_angle_3_deg18.347
r_dihedral_angle_1_deg6.899
r_scangle_it3.674
r_scbond_it2.36
r_angle_refined_deg1.497
r_mcangle_it1.407
r_mcbond_it0.864
r_nbtor_refined0.301
r_symmetry_vdw_refined0.214
r_nbd_refined0.207
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.134
r_chiral_restr0.103
r_bond_refined_d0.013
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 Atoms844
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing