2F64

Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6 A resolution with 1-METHYLQUINOLIN-2(1H)-ONE 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 DROP4.627730 % PEG MME 2000, 0.2 ammonium sulfate, 0.1 sodium acetate trihydrate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6353.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.827α = 90
b = 75.351β = 90.01
c = 87.048γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL1-50.92014SSRLBL1-5

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
11.63095.640.049112.34621715.665
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)
11.61.68692.530.1652.22.26400

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 2A0K1.63046217248495.640.16630.16630.16520.18712RANDOM13.735
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]
-0.010.04-0.040.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.509
r_dihedral_angle_4_deg15.864
r_dihedral_angle_3_deg10.64
r_dihedral_angle_1_deg4.869
r_scangle_it3.146
r_scbond_it2.203
r_mcangle_it1.486
r_mcbond_it1.437
r_angle_refined_deg0.934
r_angle_other_deg0.728
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.509
r_dihedral_angle_4_deg15.864
r_dihedral_angle_3_deg10.64
r_dihedral_angle_1_deg4.869
r_scangle_it3.146
r_scbond_it2.203
r_mcangle_it1.486
r_mcbond_it1.437
r_angle_refined_deg0.934
r_angle_other_deg0.728
r_mcbond_other0.241
r_symmetry_vdw_other0.24
r_nbd_refined0.213
r_nbtor_refined0.182
r_nbd_other0.166
r_symmetry_vdw_refined0.1
r_xyhbond_nbd_refined0.097
r_symmetry_hbond_refined0.088
r_nbtor_other0.081
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms374
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing