4PDJ

Neutron crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RX2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729140mg/mL DHFR-folate-NADP+ complex, 12% (v/v) PEG400, 100 mM MnCl2, 20 mM imidazole, pH7.0
Crystal Properties
Matthews coefficientSolvent content
2.1542.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.293α = 90
b = 45.625β = 90
c = 98.974γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291IMAGE PLATERIGAKUmirrors2013-09-10MSINGLE WAVELENGTH
21neutron291CUSTOM-MADEmirrors2013-08-10LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54
2NUCLEAR REACTOROTHER3.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)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
11.5993079.30.1885.37.5207513.2
21.99432.4701.21.28745
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.5991.70.313.25.8
21.9942.1

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (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 REPLACEMENT1.59927.41320751106897.580.19480.19370.218
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT1.99432.403874342778.420.23220.23030.2707
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
f_dihedral_angle_d19.963
f_angle_d0.915
f_bond_d0.092
f_chiral_restr0.039
f_plane_restr0.028
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1268
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms82

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-3000data processing
Cootmodel building
PDB_EXTRACTdata extraction
Cootmodel building
SCALAdata reduction
PHASERphasing
SCALAdata scaling
LAUEGENdata reduction