2C2T

Human Dihydrofolate Reductase Complexed With NADPH and 2,4-Diamino-5-((7,8-dicarbaundecaboran-7-yl)methyl)-6-methylpyrimidine, a novel boron containing, nonclassical Antifolate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherUNPUBLISHED HUMAN DHFR STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8277THE TERNARY COMPLEX OF DHFR WITH NADPH AND 39B WAS FORMED BY MIXING HUMAN DHFR (20 MG/ML IN 25 MM KPO4 (PH 7.0), 0.1 MM EDTA, AND 3 MM NAN3) WITH 60 MM NADPH, FOLLOWED 15 MINUTES LATER BY 60 MM OF INHIBITOR IN DMSO (FINAL CONCENTRATIONS OF 2 MM NADPH AND 2 MM INHIBITOR). THIS COMPLEX SOLUTION WAS MIXED WITH AN EQUAL VOLUME OF PRECIPITANT CONTAINING 24-33% PEG 4000, 0.2 M LI2SO4, 0.1 M TRIS CL (PH 7.9-8.4), 5% GLYCEROL, AND EQUILIBRATED WITH THE PRECIPITANT BY HANGING DROP VAPOR DIFFUSION AT 277 K. THE CRYSTAL GREW IN ABOUT 3 WEEKS. THE CRYSTAL WAS FLASH-COOLED DIRECTLY IN LIQUID NITROGEN AFTER HARVESTING INTO MOTHER LIQUOR CONTAINING 10% GLYCEROL. NOTE THAT THE INHIBITOR IS ACTUALLY A RACEMIC MIXTURE OF 39B AND ITS ENANTIOMER, HERE CALLED 39E. IT IS THE RACEMATE THAT IS BOUND IN THE CRYSTAL, REPRESENTED IN THE COORDINATES AS A 1:1 STATISTICALLY-DISORDERED MIXTURE OF 39B AND 39E.
Crystal Properties
Matthews coefficientSolvent content
2.346.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.628α = 90
b = 94.354β = 90
c = 96.032γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRROR1999-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-1SSRLBL9-1

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
11.53598.40.068.42.96259419
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)
11.51.5490.10.451.72.1

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 REPLACEMENTTHROUGHOUTUNPUBLISHED HUMAN DHFR STRUCTURE1.52059389316898.10.160.1580.213RANDOM17.53
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]
-0.190.52-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.148
r_dihedral_angle_3_deg12.361
r_dihedral_angle_4_deg12.057
r_dihedral_angle_1_deg5.892
r_scangle_it3.438
r_scbond_it2.642
r_mcangle_it1.684
r_angle_refined_deg1.451
r_mcbond_it1.413
r_angle_other_deg1.202
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.148
r_dihedral_angle_3_deg12.361
r_dihedral_angle_4_deg12.057
r_dihedral_angle_1_deg5.892
r_scangle_it3.438
r_scbond_it2.642
r_mcangle_it1.684
r_angle_refined_deg1.451
r_mcbond_it1.413
r_angle_other_deg1.202
r_mcbond_other0.557
r_symmetry_hbond_refined0.204
r_nbd_refined0.201
r_nbd_other0.194
r_symmetry_vdw_other0.18
r_nbtor_refined0.176
r_symmetry_vdw_refined0.144
r_xyhbond_nbd_refined0.141
r_chiral_restr0.09
r_nbtor_other0.084
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_xyhbond_nbd_other0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms3004
Nucleic Acid Atoms
Solvent Atoms607
Heterogen Atoms186

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing