6KOT

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with B12128 and NADPH

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	4.5	297	NaOAc, NH2OAc, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.176	α = 90
b = 156.175	β = 90
c = 165.08	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		2016-10-14	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)	R Merge I (Observed)	Rrim I (All)	Rpim I (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	2.149	50	85	0.058	0.067	0.033	19.75	3.7		67136

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	2.15	2.23	86.2		0.403	0.908		3.1

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	4DP3	2.149	45.047	66982	3355	82.177	0.196	0.1936	0.249	31.803

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]
0.516			-0.081		-0.435

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.702
r_dihedral_angle_3_deg	16.657
r_dihedral_angle_4_deg	15.685
r_dihedral_angle_1_deg	8.303
r_lrange_it	7.185
r_lrange_other	7.18
r_scangle_it	4.68
r_scangle_other	4.68
r_mcangle_it	4.328
r_mcangle_other	4.328
r_scbond_it	3
r_scbond_other	2.994
r_mcbond_it	2.786
r_mcbond_other	2.786
r_chiral_restr_other	1.973
r_angle_refined_deg	1.702
r_angle_other_deg	1.314
r_symmetry_nbd_refined	0.251
r_nbd_other	0.218
r_nbd_refined	0.211
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.161
r_chiral_restr	0.126
r_symmetry_xyhbond_nbd_other	0.094
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8722
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms	196

Software

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