6LEU | pdb_00006leu

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with compound 42 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	4.6	298	0.1M sodium acetate, pH 4.6, 0.2M ammonium acetate, 25% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.308	α = 90
b = 154.488	β = 90
c = 163.939	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	Nonius Kappa CCD		2003-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ENRAF-NONIUS FR591	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	2.59	10	90.8	0.071	14.5	3.99		40994

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	2.65	2.74			0.479

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	4DP3	2.59	10	40185	2053	88.369	0.193	0.1889	0.19	0.2609	0.26	39.937

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]
1.514			-1.818		0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.278
r_dihedral_angle_4_deg	18.488
r_dihedral_angle_3_deg	18.19
r_dihedral_angle_1_deg	9.078
r_lrange_other	8.958
r_lrange_it	8.957
r_mcangle_it	6.404
r_mcangle_other	6.404
r_scangle_it	5.598
r_scangle_other	5.598
r_mcbond_it	3.972
r_mcbond_other	3.965
r_scbond_it	3.544
r_scbond_other	3.544
r_angle_refined_deg	1.79
r_angle_other_deg	1.259
r_chiral_restr_other	0.753
r_nbd_other	0.24
r_symmetry_nbd_refined	0.222
r_nbd_refined	0.215
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.153
r_chiral_restr	0.116
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8875
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	194

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
Coot	model building
HKL-2000	data scaling