2F2T

Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.7 A resolution with 5-Aminoisoquinoline bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A0Kpdb entry 2A0K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.629830 % PEG MME 2000 0.2 ammonium sulfate 0.1 sodium acetate trihydrate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5752.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.96α = 90
b = 75.493β = 90.05
c = 86.324γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.92020ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.73092.830.06610.73.13674018.141
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.79267.240.2173.92.23881

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2A0K1.73036740192892.830.177940.177940.176560.20373RANDOM13.905
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]
-0.07-0.110.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.344
r_dihedral_angle_4_deg14.392
r_dihedral_angle_3_deg10.424
r_dihedral_angle_1_deg4.655
r_scangle_it2.562
r_scbond_it1.735
r_mcangle_it1.325
r_mcbond_it1.155
r_angle_refined_deg0.863
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.344
r_dihedral_angle_4_deg14.392
r_dihedral_angle_3_deg10.424
r_dihedral_angle_1_deg4.655
r_scangle_it2.562
r_scbond_it1.735
r_mcangle_it1.325
r_mcbond_it1.155
r_angle_refined_deg0.863
r_nbtor_refined0.301
r_symmetry_hbond_refined0.229
r_nbd_refined0.181
r_symmetry_vdw_refined0.129
r_xyhbond_nbd_refined0.077
r_chiral_restr0.063
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2518
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing