8YQ8 | pdb_00008yq8

Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB8, 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	4DP3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	4.6	297	0.1 M Sodium acetate, pH 4.6, 0.2 M Ammonium acetate, 12% Polyethylene glycol 4000

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.763	α = 90
b = 156.41	β = 90
c = 165.065	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		2022-03-24	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	2.1	26.1	99.32	0.082	0.998	13.5	5.9		88097

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	100		0.487	0.915	2.4	4.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	26.096	87705	4422	99.352	0.197	0.1945	0.2036	0.2404	0.2452	RANDOM	33.374

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]
-0.144			0.037		0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.47
r_dihedral_angle_3_deg	14.045
r_dihedral_angle_2_deg	11.763
r_lrange_it	8.301
r_lrange_other	8.264
r_dihedral_angle_1_deg	7.46
r_scangle_it	5.847
r_scangle_other	5.847
r_mcangle_it	4.357
r_mcangle_other	4.357
r_scbond_it	3.795
r_scbond_other	3.787
r_mcbond_it	2.988
r_mcbond_other	2.987
r_dihedral_angle_other_2_deg	2.735
r_angle_refined_deg	1.834
r_angle_other_deg	0.613
r_nbd_other	0.224
r_symmetry_nbd_refined	0.223
r_nbd_refined	0.215
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_refined	0.079
r_symmetry_xyhbond_nbd_other	0.075
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8676
Nucleic Acid Atoms
Solvent Atoms	588
Heterogen Atoms	198

Software

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