1W25

Response regulator PleD in complex with c-diGMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.2CRYSTALS WERE OBTAINED AT ROOM TEMPERATURE BY HANGING DROP VAPOUR DIFFUSION. FOR THIS, PLED AT A NOMINAL CONCENTRATION OF 10 MG/ML IN 20 MM TRIS-HCL (PH 8.0), 100 MM NACL, 1 MM DTT, 2 MM MGCL2 AND 0.8 MM C-DIGMP6 WAS MIXED WITH THE RESERVOIR (1.0 M GLYCINE PH 9.2, 2 % DIOXANE, 14.5 % POLYETHYLENE GLYCOL 20K) AT A RATIO 1 TO 1.
Crystal Properties
Matthews coefficientSolvent content
3.969

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.87α = 90
b = 135.87β = 90
c = 169.247γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-12-14MSINGLE 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
12.760.8699.30.0816.425.743706-3.7
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)
12.72.7298.70.362.965.48

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.75041469220298.90.2120.210.239RANDOM25.61
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]
-0.07-0.070.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.956
r_dihedral_angle_4_deg16.945
r_dihedral_angle_3_deg16.4
r_dihedral_angle_1_deg5.586
r_scangle_it3.706
r_scbond_it2.416
r_mcangle_it1.307
r_angle_refined_deg1.211
r_mcbond_it1.129
r_angle_other_deg0.773
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.956
r_dihedral_angle_4_deg16.945
r_dihedral_angle_3_deg16.4
r_dihedral_angle_1_deg5.586
r_scangle_it3.706
r_scbond_it2.416
r_mcangle_it1.307
r_angle_refined_deg1.211
r_mcbond_it1.129
r_angle_other_deg0.773
r_symmetry_vdw_other0.295
r_nbd_refined0.201
r_mcbond_other0.18
r_symmetry_vdw_refined0.177
r_nbd_other0.17
r_xyhbond_nbd_refined0.108
r_nbtor_other0.083
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms6962
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms233

Software

Software
Software NamePurpose
DMmodel building
TRUNCATEdata scaling
SHELXDphasing
SHARPphasing
SOLOMONphasing
DMphasing
REFMACrefinement