7CTY

Wild type plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS), fragment 263, NADP+, 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, 13%PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.5864038	52.473164

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.143	α = 90
b = 154.088	β = 90
c = 163.598	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		2019-09-18	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	2.641	24.527	96.7	0.0927	12.68	4.66		34592			17.16

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	2.8	2.94	88.4		0.1876

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	2.8	20.7	34591	1686	81.167	0.238	0.2343	0.3031	27.023

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]
-3.219			11.71		-8.491

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.128
r_dihedral_angle_3_deg	19.933
r_dihedral_angle_4_deg	17.233
r_dihedral_angle_1_deg	9.063
r_lrange_it	6.266
r_lrange_other	6.266
r_mcangle_other	4.166
r_mcangle_it	4.165
r_scangle_other	3.459
r_scangle_it	3.416
r_mcbond_it	2.465
r_mcbond_other	2.464
r_angle_other_deg	2.365
r_scbond_it	1.976
r_scbond_other	1.976
r_angle_refined_deg	1.647
r_chiral_restr_other	1.46
r_nbd_other	0.306
r_symmetry_nbd_refined	0.283
r_symmetry_nbd_other	0.226
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.201
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.114
r_symmetry_xyhbond_nbd_other	0.107
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.07
r_bond_other_d	0.035
r_bond_refined_d	0.008
r_gen_planes_other	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8658
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	86

Software

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