2W3B

HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND A LIPOPHILIC ANTIFOLATE SELECTIVE FOR MYCOBACTERIUM AVIUM DHFR, 6-((2,5- DIETHOXYPHENYL)AMINOMETHYL)-2,4-DIAMINO-5-METHYLPYRIDO(2,3-D) PYRIMIDINE (SRI-8686)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherUNPUBLISHED HUMAN DHFR FOLATE COMPLEX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.75277HUMAN DHFR/FOLATE COMPLEX WAS MIXED WITH NADPH AND 6-((2,5-DIETHOXYPHENYL)AMINOMETHYL)-2, 4-DIAMINO-5-METHYLPYRIDO(2,3-D)PYRIMIDINE (SRI-8686) (BOTH 2 MM FINAL). CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION AT 277 K BY MIXING EQUAL VOLUMES OF PROTEIN/NADPH/SRI-8686 WITH RESERVOIR (24% PEG 4000, 200 MM LI2SO4, 100 MM TRIS.HCL, PH 8.75). TRUNCATED TRIANGULAR CRYSTALS APPEARED SLOWLY, IN ABOUT A MONTH. THE CRYSTAL WAS CRYOPROTECTED WITH 15% GLYCEROL AND FLASH-COOLED IN LIQUID N2.
Crystal Properties
Matthews coefficientSolvent content
2.346.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.725α = 90
b = 94.387β = 90
c = 95.439γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2000-01-18MSINGLE 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
11.251598.90.0510.13.4109188-1016.1
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)
11.251.28880.711.42.8

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 FOLATE COMPLEX1.2714.9598560525199.80.1720.1710.203RANDOM16.01
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]
-0.230.46-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.887
r_dihedral_angle_3_deg11.058
r_dihedral_angle_4_deg10.274
r_dihedral_angle_1_deg6.151
r_scangle_it3.718
r_scbond_it2.768
r_mcangle_it1.95
r_angle_refined_deg1.648
r_mcbond_it1.275
r_angle_other_deg1.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.887
r_dihedral_angle_3_deg11.058
r_dihedral_angle_4_deg10.274
r_dihedral_angle_1_deg6.151
r_scangle_it3.718
r_scbond_it2.768
r_mcangle_it1.95
r_angle_refined_deg1.648
r_mcbond_it1.275
r_angle_other_deg1.228
r_symmetry_vdw_other0.253
r_symmetry_vdw_refined0.231
r_nbd_refined0.225
r_nbd_other0.205
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.143
r_chiral_restr0.096
r_nbtor_other0.085
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.002
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_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 Atoms2917
Nucleic Acid Atoms
Solvent Atoms573
Heterogen Atoms216

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing