8PQR

Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 WT bound to DAD_Immucillin-H


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 DROP6.5293.1528% v/v PEG Smear Broad; 0.1 M Tris pH 8.5; 0.15 M Ammonium Acetate; 0.01 M Calcium chloride dihydrate
Crystal Properties
Matthews coefficientSolvent content
2.5251.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.28α = 90
b = 97.28β = 90
c = 65.85γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS EIGER2 XE 16M2022-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.58651.8821000.1210.1270.0390.9988.710.194410
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.5861.61399.91.2352.8171.0820.40.76.5

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.58651.8821.9893627453899.160.17140.17010.1966
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_d6.257
f_angle_d0.922
f_chiral_restr0.059
f_bond_d0.007
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4979
Nucleic Acid Atoms
Solvent Atoms470
Heterogen Atoms76

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXphasing
autoPROCdata processing
autoPROCdata scaling
XDSdata reduction