6KP2

Quadruple mutant plasmodium falciparum dihydrofolate reductase complexed with B10042

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		297	NaOAc, NH2OAc, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.995	α = 90
b = 155.944	β = 90
c = 165.34	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		2016-10-15	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	1.97	50	99.7	0.032	0.038	0.02	19.8	3.8		104189

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	1.97	2.04	99.9		0.161	0.188	0.096	0.979		3.8

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	1.973	32.199	103923	5079	99.352	0.175	0.173	0.2129	29.648

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]
-0.071			0.123		-0.051

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.925
r_dihedral_angle_4_deg	17.988
r_dihedral_angle_3_deg	16.025
r_lrange_it	7.817
r_lrange_other	7.817
r_dihedral_angle_1_deg	7.671
r_scangle_it	5.63
r_scangle_other	5.616
r_mcangle_it	4.502
r_mcangle_other	4.502
r_scbond_it	3.703
r_scbond_other	3.691
r_mcbond_it	3.095
r_mcbond_other	3.079
r_angle_refined_deg	1.807
r_angle_other_deg	1.401
r_chiral_restr_other	0.934
r_nbd_other	0.255
r_symmetry_nbd_refined	0.218
r_nbd_refined	0.212
r_symmetry_xyhbond_nbd_refined	0.212
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.144
r_symmetry_xyhbond_nbd_other	0.081
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8757
Nucleic Acid Atoms
Solvent Atoms	716
Heterogen Atoms	168

Software

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