7F3Z | pdb_00007f3z

Double mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS-K1, C59R+S108N) complexed with Trimethoprim (TOP), NADPH and dUMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QGT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		297	28.5% PEG4000, 0.8 M CH3COONH4 0.08 M CH3COONa

Crystal Properties
Matthews coefficient	Solvent content
2.47	55.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.332	α = 90
b = 153.739	β = 90
c = 164.119	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	IMAGE PLATE	RIGAKU RAXIS		2003-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU R-AXIS IV	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	CC (Half)	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	2.6	51.54	97	0.083	0.994	10.1	4.17		43724

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69			0.523

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	FREE R-VALUE	3QGT	2.6	39.782	43660	2178	97.373	0.201	0.1979	0.21	0.2531	0.26	57.552

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]
0.322			-0.724		0.402

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.228
r_dihedral_angle_3_deg	19.775
r_dihedral_angle_4_deg	18.773
r_lrange_it	8.255
r_lrange_other	8.242
r_dihedral_angle_1_deg	8.213
r_scangle_it	5.915
r_scangle_other	5.915
r_mcangle_it	5.714
r_mcangle_other	5.713
r_dihedral_angle_other_2_deg	4.694
r_scbond_it	3.869
r_scbond_other	3.869
r_mcbond_it	3.772
r_mcbond_other	3.768
r_angle_refined_deg	1.602
r_angle_other_deg	1.166
r_symmetry_nbd_refined	0.248
r_nbd_other	0.24
r_nbd_refined	0.21
r_symmetry_nbd_other	0.189
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.114
r_symmetry_xyhbond_nbd_other	0.096
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9110
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	190

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing