2V0N

ACTIVATED RESPONSE REGULATOR PLED IN COMPLEX WITH C-DIGMP AND GTP- ALPHA-S


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W25PDB ENTRY 1W25

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18PROTEIN SOLUTION: 100 MICROM PLED, 0.2 MM C-DI-GMP, 1 MM GTP-ALPHA-S, 1 MM BECL2, 10 MM NAF, 10 MM MGCL2 RESERVOIR: 0.1 M HEPES, PH 8.0, 0.73 M NA2SO4
Crystal Properties
Matthews coefficientSolvent content
3.868

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.965α = 90
b = 132.557β = 90
c = 88.425γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
12.77395.60.16.13.0239328
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)
12.72.8580.20.466.052.58

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 1W252.7130373021969940.2160.2150.252RANDOM35.58
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]
0.01-2.082.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.258
r_dihedral_angle_4_deg17.955
r_dihedral_angle_3_deg17.933
r_dihedral_angle_1_deg5.756
r_scangle_it4.154
r_scbond_it2.725
r_mcangle_it1.515
r_angle_refined_deg1.505
r_mcbond_it1.279
r_angle_other_deg1.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.258
r_dihedral_angle_4_deg17.955
r_dihedral_angle_3_deg17.933
r_dihedral_angle_1_deg5.756
r_scangle_it4.154
r_scbond_it2.725
r_mcangle_it1.515
r_angle_refined_deg1.505
r_mcbond_it1.279
r_angle_other_deg1.007
r_symmetry_hbond_refined0.229
r_nbd_refined0.223
r_symmetry_vdw_other0.22
r_nbd_other0.193
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.145
r_chiral_restr0.091
r_nbtor_other0.09
r_symmetry_vdw_refined0.084
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7012
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms272

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing