8YSU

Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB in complex with CTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8YSS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1 M BIS-TRIS propane pH 9.0, 30% w/v Polyethylene glycol 6,000.
Crystal Properties
Matthews coefficientSolvent content
2.3247.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.363α = 90
b = 111.506β = 100.415
c = 46.981γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 07A0.97624NSRRCTPS 07A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.943098.20.99515.4246.525742
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.942.010.705

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.94423.88125173124595.6350.2040.20210.238926.792
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]
-0.010.269-0.032-0.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.034
r_dihedral_angle_3_deg14.941
r_dihedral_angle_4_deg13.682
r_lrange_it8.356
r_lrange_other8.335
r_dihedral_angle_1_deg6.658
r_scangle_it4.909
r_scangle_other4.908
r_mcangle_other3.413
r_mcangle_it3.412
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2647
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data scaling