3NRR

Co-crystal structure of dihydrofolate reductase-thymidylate synthase from Babesia bovis with dUMP, Raltitrexed and NADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K2HPDB ENTRY 3K2H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52891:1 CO-CRYSTALLIZATION DROP. PROTEIN SOLUTION: 20 MG/ML PROTEIN, 2.0MM DUMP, 2.0MM NADP, 5.0MM RALTITREXED, 0.5M SODIUM CHLORIDE, 0.025M HEPES, 5%(V/V) GLYCEROL, 2.0MM DITHIOTHREITOL. CRYSTALLANT SOLUTION (HT INDEX E11): 0.02M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1M HEPES, 22%(W/V) POLY(ACRYLIC ACID) SODIUM SALT 5100, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties
Matthews coefficientSolvent content
2.652.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.33α = 119.61
b = 83.83β = 102.04
c = 83.92γ = 90.26
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.99740ALS5.0.1

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
11.85097.20.0612.32108796
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)
11.81.8395.90.3542.439210489

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3K2H1.819.94108796104245557398.520.19560.19350.236RANDOM19.8103
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]
-1.910.06-0.251.51.261.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.942
r_dihedral_angle_4_deg20.686
r_dihedral_angle_3_deg12.993
r_dihedral_angle_1_deg6.392
r_scangle_it3.202
r_scbond_it2.129
r_angle_refined_deg1.753
r_mcangle_it1.291
r_angle_other_deg0.982
r_mcbond_it0.758
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.942
r_dihedral_angle_4_deg20.686
r_dihedral_angle_3_deg12.993
r_dihedral_angle_1_deg6.392
r_scangle_it3.202
r_scbond_it2.129
r_angle_refined_deg1.753
r_mcangle_it1.291
r_angle_other_deg0.982
r_mcbond_it0.758
r_mcbond_other0.246
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7965
Nucleic Acid Atoms
Solvent Atoms1025
Heterogen Atoms329

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
PHASESphasing