Experiment: 6P9Z

Staphylococcus aureus Dihydrofolate reductase in complex with NADPH and Methotrexate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F0Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	278	0.1 M MES, pH 5.5 0.2 M sodium acetate 15% PEG 10,000 20% gamma-butyrolactone, additive

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.033	α = 90
b = 79.033	β = 90
c = 109.093	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	100	CCD	MARMOSAIC 325 mm CCD	image plate	2017-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.95	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.86	32.11	99.28	40.8	14.1		17420

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.92	98.48

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3F0Q	1.86	32.11	1.34	17429	1743	99.32	0.1924	0.1894	0.1896	0.2186	0.2194

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.682
f_angle_d	1.039
f_chiral_restr	0.067
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1273
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	87

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing