8YQ9

Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB6, NADPH and dUMP

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DP3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		297	0.1M Sodium malonate, pH5.0, 14% Polyethylene glycol 4000

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.064	α = 90
b = 156.496	β = 90
c = 164.865	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	CMOS	BRUKER PHOTON 100		2021-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER TURBO X-RAY SOURCE	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	24.63	99.1	0.135	0.995	9.1	5.9		59549			31.73

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	2.4	2.45	92.5		0.873	2	5.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.4	24.629	58306	2903	97.567	0.221	0.2171	0.2909	RANDOM	40.802

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]
0.51			-0.421		-0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.167
r_dihedral_angle_6_deg	14.102
r_dihedral_angle_2_deg	10.508
r_lrange_it	9.965
r_lrange_other	9.961
r_dihedral_angle_1_deg	7.754
r_scangle_it	5.984
r_scangle_other	5.983
r_mcangle_it	5.475
r_mcangle_other	5.475
r_scbond_it	3.809
r_scbond_other	3.784
r_mcbond_it	3.567
r_mcbond_other	3.567
r_angle_refined_deg	1.819
r_dihedral_angle_other_2_deg	0.966
r_angle_other_deg	0.618
r_nbd_other	0.256
r_nbd_refined	0.221
r_symmetry_nbd_refined	0.212
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.196
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_refined	0.072
r_symmetry_xyhbond_nbd_other	0.045
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	8684
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	208

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing