3MF4

Crystal structure of putative two-component system response regulator/ggdef domain protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LUFPDB entry 3LUF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529820% PEG 8000, 0.1 M Tris, 0.2 M MgCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8232.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.919α = 61.95
b = 53.269β = 81.09
c = 57.908γ = 78.76
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-04-29SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9791NSLSX29A

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
11.85086.20.0711.21.933709
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)
11.81.8358.90.291.91180

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 3LUF1.82033220166285.070.2240.2220.273RANDOM12.726
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]
-0.19-0.20.030.47-0.340.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.798
r_dihedral_angle_4_deg16.413
r_dihedral_angle_3_deg15.171
r_scbond_it7.613
r_dihedral_angle_1_deg5.515
r_mcangle_it3.281
r_scangle_it1.303
r_angle_refined_deg1.285
r_mcbond_it1.049
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.798
r_dihedral_angle_4_deg16.413
r_dihedral_angle_3_deg15.171
r_scbond_it7.613
r_dihedral_angle_1_deg5.515
r_mcangle_it3.281
r_scangle_it1.303
r_angle_refined_deg1.285
r_mcbond_it1.049
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3898
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms4

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction