Experiment: 8YSI

 8YSI

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


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
2.3447.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.375α = 101.796
b = 46.302β = 106.802
c = 60.792γ = 95.768
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2021-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A0.99984NSRRCTPS 05A

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
11.8973094.70.03821.8652.426575
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)
11.8971.970.983

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 REPLACEMENTTHROUGHOUT1.89723.45226517132093.9750.1770.17520.20724.106
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]
0.095-0.0150.146-0.18-0.3010.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.389
r_dihedral_angle_4_deg16.556
r_dihedral_angle_3_deg14.466
r_dihedral_angle_1_deg6.731
r_lrange_it6.547
r_lrange_other6.466
r_scangle_it4.859
r_scangle_other4.858
r_mcangle_it3.371
r_mcangle_other3.371
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2616
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms58

Software

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