2C2S

Human Dihydrofolate Reductase Complexed With NADPH and 2,4-Diamino-5-(1-o-carboranylmethyl)-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 34B 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.
Crystal Properties
Matthews coefficientSolvent content
2.346.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.671α = 90
b = 93.864β = 90
c = 95.782γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRROR1999-03-02MSINGLE 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
11.435840.0511.236530016.1
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)
11.41.4443.10.461.51.3

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 STRUCTURE1.42061984326083.90.1570.1550.198RANDOM19.68
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]
-0.160.18-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.123
r_dihedral_angle_3_deg12.65
r_dihedral_angle_4_deg12.302
r_dihedral_angle_1_deg6.022
r_angle_refined_deg1.553
r_angle_other_deg1.213
r_nbd_refined0.203
r_symmetry_vdw_other0.202
r_nbd_other0.192
r_nbtor_refined0.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.123
r_dihedral_angle_3_deg12.65
r_dihedral_angle_4_deg12.302
r_dihedral_angle_1_deg6.022
r_angle_refined_deg1.553
r_angle_other_deg1.213
r_nbd_refined0.203
r_symmetry_vdw_other0.202
r_nbd_other0.192
r_nbtor_refined0.177
r_symmetry_vdw_refined0.174
r_symmetry_hbond_refined0.147
r_xyhbond_nbd_refined0.132
r_chiral_restr0.094
r_nbtor_other0.085
r_bond_refined_d0.014
r_gen_planes_refined0.007
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms2962
Nucleic Acid Atoms
Solvent Atoms556
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing