6ZXM

Diguanylate cyclase DgcR in complex with c-di-GMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V0N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5291.150.2 M Potassium thiocyanate; 0.1 M Tris pH 7.5; 25% PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.2946.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.603α = 90
b = 72.917β = 118.2
c = 125.729γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93.15PIXELDECTRIS PILATUS 2M-F2017-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

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
13.348990.166.753.782803874
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)
13.33.491.780.682

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 REPLACEMENTTHROUGHOUT2V0N3.330280381503990.2280.2250.299RANDOM90.38
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]
2.990.99-0.13-2.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.523
r_dihedral_angle_3_deg22.542
r_dihedral_angle_4_deg20.326
r_dihedral_angle_1_deg8.603
r_angle_refined_deg1.988
r_angle_other_deg1.225
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.523
r_dihedral_angle_3_deg22.542
r_dihedral_angle_4_deg20.326
r_dihedral_angle_1_deg8.603
r_angle_refined_deg1.988
r_angle_other_deg1.225
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14070
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms558

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing