6NXZ

Crystal structure of trimethoprim-resistant type II dihydrofolate reductase in complex with a bisbenzimidazole inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	The protein concentration was adjusted from 13.3 mg/ml to 10 mg/mL by addition of a final concentration of 25% MPD. Reservoirs were prepared in Eppendorf tubes with 100mM Tris-Cl pH 8.0 55% MPD in a Greiner 24-well hanging-drop crystallization plate. On a siliconized glass cover slip (Hampton Research), 2.0 uL of protein solution were combined with 2.0 uL of the reservoir solution. The plate was incubated at 277 K, and crystals were obtained after 3-4 days.

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.617	α = 90
b = 67.617	β = 90
c = 51.977	γ = 90

Symmetry
Space Group	I 41 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	93	CCD	RIGAKU SATURN 944+	VariMax HF	2014-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.75	50	94.3	0.204	0.205	0.02	4.6	79.2		6007

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	1.75	1.78	48.7		0.697		1.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2RH2	1.75	47.86	5681	319	94.27	0.1785	0.1768	0.2082	RANDOM	21.063

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]
0.12			0.12		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.412
r_dihedral_angle_3_deg	16.031
r_dihedral_angle_4_deg	14.721
r_dihedral_angle_1_deg	6.246
r_angle_refined_deg	2.061
r_angle_other_deg	0.947
r_chiral_restr	0.111
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.412
r_dihedral_angle_3_deg	16.031
r_dihedral_angle_4_deg	14.721
r_dihedral_angle_1_deg	6.246
r_angle_refined_deg	2.061
r_angle_other_deg	0.947
r_chiral_restr	0.111
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	418
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	26

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

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 R01GM133198.