Experiment: 8YSK

 8YSK

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherapo DwCdnB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2 M MOPS pH 6.5, 20% w/v Polyethylene glycol 4,000.
Crystal Properties
Matthews coefficientSolvent content
2.346.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.274α = 101.137
b = 46.091β = 106.903
c = 59.889γ = 95.429
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 07A0.97626NSRRCTPS 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
11.9843096.40.997256.623181
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)
11.9842.060.965

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 REPLACEMENTTHROUGHOUT1.98423.24522117109291.4040.1690.16670.209229.829
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]
0.034-0.2620.263-0.418-0.6830.481
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.805
r_dihedral_angle_3_deg15.019
r_dihedral_angle_4_deg14.098
r_dihedral_angle_1_deg6.738
r_lrange_it6.116
r_lrange_other6.074
r_scangle_it4.739
r_scangle_other4.737
r_mcangle_it3.505
r_mcangle_other3.504
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2647
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms31

Software

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