Experiment: 8YSO

 8YSO

Crystal structure of the Deinococcus wulumuqiensis CD-NTase DwCdnB Ear-cut mutant in complex with ATP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1 M Bis-Tris pH 6.5, 0.2 M Sodium fluoride, 23 % w/v PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.3146.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.331α = 90
b = 72.832β = 90
c = 100.998γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 07A0.97625NSRRCTPS 07A

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
11.683099.40.05847.0671242038
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)
11.681.740.917

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 REPLACEMENTTHROUGHOUT1.6823.97341873211899.0560.1720.17090.199416.584
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]
0.1660.11-0.276
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.933
r_dihedral_angle_4_deg15.4
r_dihedral_angle_3_deg12.471
r_dihedral_angle_1_deg6.649
r_lrange_it5.826
r_lrange_other5.67
r_scangle_it4.305
r_scangle_other4.279
r_mcangle_it2.741
r_mcangle_other2.741
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2474
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms69

Software

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