3D80

Structural Analysis of a Holo Enzyme Complex of Mouse Dihydrofolate Reductase with NADPH and a Ternary Complex wtih the Potent and Selective Inhibitor 2,4-Diamino-6-(2'-hydroxydibenz[b,f]azepin-5-yl)methylpteridine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FZJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.15 M Tris, pH 8.3, 75 mM Na cacodylate, pH 6.5, 21% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2946.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.482α = 90
b = 61.3β = 117.23
c = 43.589γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMAR CCD 130 mm2006-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-11.00SSRLBL9-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.431.6198.30.0830.065.33.738237354551125
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4515.20.30.0231.522589

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2fzj1.431.61113545535455185197.570.220.200720.198820.23573RANDOM19.942
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.902
r_dihedral_angle_4_deg14.526
r_dihedral_angle_3_deg14.215
r_dihedral_angle_1_deg5.633
r_scangle_it2.963
r_scbond_it1.976
r_angle_refined_deg1.682
r_mcangle_it1.375
r_mcbond_it0.831
r_chiral_restr0.374
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.902
r_dihedral_angle_4_deg14.526
r_dihedral_angle_3_deg14.215
r_dihedral_angle_1_deg5.633
r_scangle_it2.963
r_scbond_it1.976
r_angle_refined_deg1.682
r_mcangle_it1.375
r_mcbond_it0.831
r_chiral_restr0.374
r_nbtor_refined0.308
r_symmetry_vdw_refined0.243
r_nbd_refined0.21
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.167
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1513
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing