3TVK

Diguanylate cyclase domain of DgcZ


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5293100mM Tris, 22.5% PEG 4000, pH 8.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.623α = 90
b = 79.623β = 90
c = 51.207γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DASLSX06DA

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
11.851.211000.0750.07524.112.51729219.75
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)
11.81.91000.3460.3467.612

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 ENTRY 1W251.81517232172328721000.1670.1660.201RANDOM19.5
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]
-0.21-0.11-0.210.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.862
r_dihedral_angle_4_deg13.563
r_dihedral_angle_3_deg11.863
r_scangle_it6.019
r_dihedral_angle_1_deg5.523
r_scbond_it4.094
r_mcangle_it2.894
r_mcbond_it1.815
r_angle_refined_deg1.281
r_angle_other_deg0.804
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.862
r_dihedral_angle_4_deg13.563
r_dihedral_angle_3_deg11.863
r_scangle_it6.019
r_dihedral_angle_1_deg5.523
r_scbond_it4.094
r_mcangle_it2.894
r_mcbond_it1.815
r_angle_refined_deg1.281
r_angle_other_deg0.804
r_mcbond_other0.681
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1370
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing