Experiment: 8YSG

 8YSG

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


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 sodium formate, 20 % w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0439.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.033α = 90
b = 100.404β = 101.621
c = 46.398γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2021-05-11MSINGLE 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
12.173099.30.02847.2114.216522
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)
12.172.250.979

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 REPLACEMENTTHROUGHOUT2.17122.7341649882499.3560.2430.24170.271837.635
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]
-0.014-0.022-0.0790.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.299
r_dihedral_angle_4_deg18.475
r_dihedral_angle_3_deg17.559
r_lrange_it8.982
r_lrange_other8.982
r_dihedral_angle_1_deg8.126
r_mcangle_it5.25
r_mcangle_other5.249
r_scangle_it4.702
r_scangle_other4.701
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2585
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms66

Software

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