3I8A | pdb_00003i8a

Staphylococcus aureus H30N, F98Y Dihydrofolate Reductase complexed with NADPH and 2,4-diamino-5-(3-(2,5-dimethoxyphenyl)prop-1-ynyl)-6-ethylpyrimidine (UCP120B)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	15% PEG 10,000, 150 mM sodium acetate, 100 mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.164	α = 90
b = 79.164	β = 90
c = 108.96	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		2009-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	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	2.41	37.22	95.01	0.04	0.04	1.1	10.4	7504	7504	3	3	15.689

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	2.41	2.472	100		0.074	0.074	0.8	10.1	560

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	Difference Fourier Methods	THROUGHOUT	3FQO	2.41	37.22	7504	7504	363	95.01	0.208	0.208	0.206	0.21	0.261	0.26	RANDOM	15.662

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		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.063
r_dihedral_angle_4_deg	20.893
r_dihedral_angle_3_deg	18.586
r_dihedral_angle_1_deg	7.585
r_scangle_it	2.709
r_scbond_it	1.777
r_angle_refined_deg	1.64
r_mcangle_it	1.314
r_mcbond_it	0.753
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.063
r_dihedral_angle_4_deg	20.893
r_dihedral_angle_3_deg	18.586
r_dihedral_angle_1_deg	7.585
r_scangle_it	2.709
r_scbond_it	1.777
r_angle_refined_deg	1.64
r_mcangle_it	1.314
r_mcbond_it	0.753
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.186
r_symmetry_hbond_refined	0.162
r_chiral_restr	0.105
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1272
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	71

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.