2W3M

HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND FOLATE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.75277HUMAN DHFR/FOLATE COMPLEX WAS MIXED WITH NADPH (2 MM FINAL). CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION AT 277 K BY MIXING EQUAL VOLUMES OF PROTEIN/NADPH/FOLATE 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
2.3547.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.552α = 90
b = 94.269β = 90
c = 96.681γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM-1MIRRORS1996-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A1CHESSA1

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
11.610.798.40.054.55.652618-1019.9
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)
11.61.6993.60.351.83.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1DRF1.610.749931266098.10.1690.1670.208RANDOM14.09
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]
0.010.05-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.505
r_dihedral_angle_4_deg11.845
r_dihedral_angle_3_deg11.565
r_dihedral_angle_1_deg5.917
r_scangle_it3.148
r_scbond_it2.47
r_mcangle_it1.592
r_angle_refined_deg1.583
r_mcbond_it1.343
r_angle_other_deg1.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.505
r_dihedral_angle_4_deg11.845
r_dihedral_angle_3_deg11.565
r_dihedral_angle_1_deg5.917
r_scangle_it3.148
r_scbond_it2.47
r_mcangle_it1.592
r_angle_refined_deg1.583
r_mcbond_it1.343
r_angle_other_deg1.233
r_symmetry_vdw_refined0.256
r_nbd_refined0.2
r_symmetry_vdw_other0.196
r_nbd_other0.19
r_symmetry_hbond_refined0.179
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.15
r_chiral_restr0.096
r_nbtor_other0.081
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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_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 Atoms2946
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
Agrovatadata scaling
AMoREphasing