3D84

Structural Analysis of a Holo Enzyme Complex of Mouse Dihydrofolate Reductase with NADPH and a Ternary Complex with 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 DROP7.429810 mM Hepes, pH 7.4, 17 mM Na acetate, pH 6.5, 85 mM Tris HCl, 25% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2344.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.226α = 90
b = 61.172β = 118.26
c = 43.15γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IVmirrors2004-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.938.0190.70.0340.050.0339.514934135511138
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)
11.91.9750.50.0760.4950.914750

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 REPLACEMENTTHROUGHOUT2fzj1.923.8311135511286568490.730.210.189020.186840.2289RANDOM19.16
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.374
r_dihedral_angle_4_deg18.953
r_dihedral_angle_3_deg18.719
r_dihedral_angle_1_deg8.483
r_scangle_it4.11
r_scbond_it2.767
r_angle_refined_deg2.063
r_mcangle_it1.814
r_angle_other_deg1.15
r_mcbond_it1.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.374
r_dihedral_angle_4_deg18.953
r_dihedral_angle_3_deg18.719
r_dihedral_angle_1_deg8.483
r_scangle_it4.11
r_scbond_it2.767
r_angle_refined_deg2.063
r_mcangle_it1.814
r_angle_other_deg1.15
r_mcbond_it1.096
r_nbtor_refined0.304
r_nbd_other0.27
r_nbd_refined0.218
r_symmetry_vdw_refined0.167
r_xyhbond_nbd_refined0.155
r_nbtor_other0.144
r_chiral_restr0.139
r_symmetry_hbond_refined0.115
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1513
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing