7F3Y

Wild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with methotrexate (MTX), NADPH and dUMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QGT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		297	PEG3350, litium chloride, sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.5	55.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.678	α = 90
b = 154.403	β = 90
c = 164.165	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	100	CCD	ADSC QUANTUM 315r		2013-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.25	50	96.9	0.994	12.5	6.6		66860

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.33			0.926

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3QGT	2.252	27.577	64950	3247	93.932	0.185	0.1822	0.2329	42.303

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]
-0.432			0.085		0.347

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.633
r_dihedral_angle_3_deg	17.411
r_dihedral_angle_4_deg	16.434
r_lrange_other	9.392
r_lrange_it	9.387
r_dihedral_angle_1_deg	7.755
r_mcangle_it	6.476
r_mcangle_other	6.475
r_scangle_it	6.45
r_scangle_other	6.449
r_mcbond_it	4.103
r_mcbond_other	4.103
r_scbond_it	4.093
r_scbond_other	4.092
r_dihedral_angle_other_2_deg	2.489
r_angle_refined_deg	1.613
r_angle_other_deg	1.267
r_nbd_other	0.242
r_symmetry_nbd_refined	0.239
r_nbd_refined	0.208
r_symmetry_nbd_other	0.192
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.171
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.021
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9075
Nucleic Acid Atoms
Solvent Atoms	546
Heterogen Atoms	247

Software

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