6KPR

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with B12155 inhibitor

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		298	NaOAc, NH2OAc, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.902	α = 90
b = 156.504	β = 90
c = 165.484	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	123	CCD	ADSC QUANTUM 315		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	2.1	50	99.1	0.056	0.061	0.024	14.4	6.2		88221

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	96.5		0.449	0.49	0.193	0.931		6

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	2.1	26.988	86619	4377	97.16	0.197	0.195	0.2411	34.067

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]
-0.021			0.129		-0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.485
r_dihedral_angle_4_deg	17.127
r_dihedral_angle_3_deg	16.434
r_dihedral_angle_1_deg	8.297
r_lrange_other	7.9
r_lrange_it	7.894
r_scangle_it	5.432
r_scangle_other	5.432
r_mcangle_it	4.946
r_mcangle_other	4.945
r_scbond_it	3.528
r_scbond_other	3.528
r_mcbond_it	3.27
r_mcbond_other	3.27
r_chiral_restr_other	2.062
r_angle_refined_deg	1.715
r_angle_other_deg	1.384
r_nbd_other	0.261
r_nbd_refined	0.21
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.177
r_symmetry_nbd_refined	0.177
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.156
r_chiral_restr	0.086
r_symmetry_xyhbond_nbd_other	0.082
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8894
Nucleic Acid Atoms
Solvent Atoms	332
Heterogen Atoms	212

Software

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