3F0X | pdb_00003f0x

Staphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH and 2,4-Diamino-5-[3-(3-methoxy-5-(3,5-dimethylphenyl)phenyl)but-1-ynyl]-6-methylpyrimidine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		Sa F98Y DHFR bound to folate and NADPH (Dale et al., J.Mol.Biol. 1997, structure not deposited in the PDB).

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	15 % PEG 10000, 150 mM Sodium acetate, 100 mM MES pH 6.5, 5 % Butyrlactone, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.048	α = 90
b = 79.048	β = 90
c = 108.727	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77.2	CCD	ADSC QUANTUM 315		2008-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.080900	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.6	39.53	93.4	0.075	0.075	4.2	8.3	5893	5893		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69	85.3		0.286	0.286	4.3	2.3	208

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	Sa F98Y DHFR bound to folate and NADPH (Dale et al., J.Mol.Biol. 1997, structure not deposited in the PDB).	2.6	39.53	5893	5893	293	93.53	0.214	0.214	0.212	0.21	0.255	0.26	RANDOM	15.908

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.867
r_dihedral_angle_4_deg	19.941
r_dihedral_angle_3_deg	18.948
r_dihedral_angle_1_deg	7.447
r_scangle_it	1.86
r_angle_refined_deg	1.627
r_scbond_it	1.258
r_mcangle_it	1.076
r_mcbond_it	0.589
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.867
r_dihedral_angle_4_deg	19.941
r_dihedral_angle_3_deg	18.948
r_dihedral_angle_1_deg	7.447
r_scangle_it	1.86
r_angle_refined_deg	1.627
r_scbond_it	1.258
r_mcangle_it	1.076
r_mcbond_it	0.589
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.111
r_symmetry_hbond_refined	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1274
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
Coot	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.