2C7V

Structure of Trypanosoma brucei pteridine reductase (PTR1) in ternary complex with cofactor and the antifolate methotrexate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7PROTEIN BUFFER WAS 20 MM TRIS HCL, PH 7.0 WITH 1MM NADP, 1 MM METHOTREXATE AND 20 MM DITHIOTHREITOL, PROTEIN CONCENTRATION WAS 6 MG/ML. HANGING DROP RESERVOIR SOLUTION WAS 0.1 M SODIUM CACODYLATE PH 6.5 AND 1.4 M SODIUM ACETATE.
Crystal Properties
Matthews coefficientSolvent content
2.0138.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.655α = 90
b = 90.244β = 115.76
c = 82.841γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMIRRORS2004-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
12.274.599.20.0612.42.850048
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2693.10.173.52.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPBD ENTRY 1E922.274.5447369253499.20.1570.1530.223RANDOM24.22
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]
-1.87-0.582.67-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.424
r_dihedral_angle_4_deg20.819
r_dihedral_angle_3_deg16.943
r_dihedral_angle_1_deg5.763
r_scangle_it2.349
r_scbond_it1.466
r_angle_refined_deg1.402
r_mcangle_it1.026
r_mcbond_it0.584
r_chiral_restr0.538
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.424
r_dihedral_angle_4_deg20.819
r_dihedral_angle_3_deg16.943
r_dihedral_angle_1_deg5.763
r_scangle_it2.349
r_scbond_it1.466
r_angle_refined_deg1.402
r_mcangle_it1.026
r_mcbond_it0.584
r_chiral_restr0.538
r_nbtor_refined0.297
r_symmetry_vdw_refined0.229
r_nbd_refined0.201
r_symmetry_hbond_refined0.159
r_xyhbond_nbd_refined0.154
r_bond_refined_d0.013
r_gen_planes_refined0.004
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7648
Nucleic Acid Atoms
Solvent Atoms799
Heterogen Atoms334

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing