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)
Type	Source	Accession Code	Details
experimental model	PDB	1RX2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	40mg/mL DHFR-folate-NADP+ complex, 12% (v/v) PEG400, 100 mM MnCl2, 20 mM imidazole, pH7.0

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.75

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	291	IMAGE PLATE	RIGAKU	mirrors	2013-09-10	M	SINGLE WAVELENGTH
2	1	neutron	291		CUSTOM-MADE	mirrors	2013-08-10	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54
2	NUCLEAR REACTOR	OTHER	3.3

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.599	30	79.3		0.188					5.3	7.5		20751		3.2
2	1.994	32.4	70							1.2	1.2		8745

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)	Redundancy	Number Unique Reflections (All)
1	1.599	1.7		0.31						3.2	5.8
2	1.994	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	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	1.599	27.413				20751	1068	97.58		0.1948	0.1937	0.218
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.994	32.403				8743	427	78.42		0.2322	0.2303	0.2707

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
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.963
f_angle_d	0.915
f_bond_d	0.092
f_chiral_restr	0.039
f_plane_restr	0.028

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1268
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	82

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-3000	data processing
Coot	model building
PDB_EXTRACT	data extraction
Coot	model building
SCALA	data reduction
PHASER	phasing
SCALA	data scaling
LAUEGEN	data reduction

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.