Experiment: 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	3.3-4.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.599	27.413				20751	1068	97.58		0.1948	0.1937	0.1946	0.218	0.2182
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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.