Experiment: 8YSM

 8YSM

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherapo DwCdnB

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
2.4750.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.401α = 105.45
b = 46.765β = 103.349
c = 64.182γ = 99.327
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)R Merge I (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
11.53096.70.044140.46.857942
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)
11.51.550.978

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 REPLACEMENTTHROUGHOUT1.523.50857636279196.0010.1740.17340.192719.78
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]
-0.015-0.0330.042-0.021-0.1520.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.48
r_dihedral_angle_4_deg13.974
r_dihedral_angle_3_deg13.074
r_dihedral_angle_1_deg6.528
r_lrange_it5.975
r_lrange_other5.799
r_scangle_it4.453
r_scangle_other4.432
r_mcangle_it3.211
r_mcangle_other3.21
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2647
Nucleic Acid Atoms
Solvent Atoms378
Heterogen Atoms36

Software

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