8PQS

Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 E88A Mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F62 
experimental modelPDB 3EHD 
experimental modelPDB 6EVS 
experimental modelPDB 6QAI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1521.43% PEG 6000; 0.1 M Tris; 0.5 M Zinc Chloride
Crystal Properties
Matthews coefficientSolvent content
3.3363.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.63α = 90
b = 135.63β = 90
c = 87.56γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS EIGER2 XE 16M2021-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.8970.2199.960.2940.02980.9996.438.773355
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.9298.615.9386.0260.3430.234.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9544.41.3466760323999.980.1990.19770.2237RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d6.351
f_angle_d0.873
f_chiral_restr0.059
f_plane_restr0.008
f_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4940
Nucleic Acid Atoms
Solvent Atoms391
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXphasing
xia2data reduction
xia2data scaling