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)
Type	Source	Accession Code	Details
experimental model	PDB	2FZJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.15 M Tris, pH 8.3, 75 mM Na cacodylate, pH 6.5, 21% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.33

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	CCD	MAR CCD 130 mm		2006-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	1.00	SSRL	BL9-1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.4	31.61	98.3	0.083	0.06	5.3	3.7	38237	35455	1	1	25

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)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	15.2		0.3	0.02	31.5	2	2589

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2fzj	1.4	31.61	1	1	35455	35455	1851	97.57	0.22	0.20072	0.19882	0.23573	RANDOM	19.942

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.902
r_dihedral_angle_4_deg	14.526
r_dihedral_angle_3_deg	14.215
r_dihedral_angle_1_deg	5.633
r_scangle_it	2.963
r_scbond_it	1.976
r_angle_refined_deg	1.682
r_mcangle_it	1.375
r_mcbond_it	0.831
r_chiral_restr	0.374

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.902
r_dihedral_angle_4_deg	14.526
r_dihedral_angle_3_deg	14.215
r_dihedral_angle_1_deg	5.633
r_scangle_it	2.963
r_scbond_it	1.976
r_angle_refined_deg	1.682
r_mcangle_it	1.375
r_mcbond_it	0.831
r_chiral_restr	0.374
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.243
r_nbd_refined	0.21
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.167
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1513
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms	95

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.