2HWV

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OPCPDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ
experimental modelPDB 1YS6PDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ
experimental modelPDB 1P2FPDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ
experimental modelPDB 1GXQPDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ

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