7CTW

Wild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with fragment 820, NADPH, dUMP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5	297	0.1M Na malonate, 12% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.185	α = 90
b = 154.73	β = 90
c = 163.816	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		2019-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.51	24.812	97.8	0.1395	11.7	5.68		41512

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.75	91.7		0.3911

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	NONE	4DPD	2.51	24.812	41511	2043	83.26	0.224	0.2205	0.2947	28.124

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]
-1.455			11.879		-10.424

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.771
r_dihedral_angle_3_deg	21.702
r_dihedral_angle_4_deg	20.549
r_dihedral_angle_1_deg	8.624
r_lrange_it	6.617
r_lrange_other	6.617
r_mcangle_it	4.221
r_mcangle_other	4.22
r_scangle_it	3.424
r_scangle_other	3.424
r_mcbond_it	2.501
r_mcbond_other	2.501
r_angle_other_deg	2.334
r_scbond_it	2.011
r_scbond_other	2.007
r_angle_refined_deg	1.693
r_chiral_restr_other	1.445
r_nbd_other	0.273
r_symmetry_xyhbond_nbd_refined	0.24
r_symmetry_nbd_other	0.232
r_nbd_refined	0.214
r_symmetry_nbd_refined	0.214
r_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.179
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.068
r_bond_other_d	0.035
r_bond_refined_d	0.009
r_gen_planes_other	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8797
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	115

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
Coot	model building