6NY0 | pdb_00006ny0

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RH2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	The protein was concentrated to 20 mg/mL in 100 mM Tris pH 8.0. Immediately before crystallization, chymotrypsin was added to the sample in a ratio of 1:100 chymotrypsin:protein, and the protein was diluted to 15 mg/mL using MPD, resulting in a final MPD concentration of 25%. Reservoirs were prepared using 750 uL of 100 mM sodium phosphate pH 7.6 and 60% MPD in a Greiner 24-well hanging-drop crystallization plate. On a siliconized glass cover slip (Hampton Research), 1.5 uL of protein were combined with 2.5 uL of reservoir solution and suspended over the well. The plate was incubated at 277 K and crystals were obtained in a few days.

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.492	α = 90
b = 67.492	β = 90
c = 51.791	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	RAYONIX MX300HE	Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips	2011-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.35	50	100	0.102	8.8	20.1		13545

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	1.35	1.37	100			14.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2RH2	1.4	41.09	11543	624	99.62	0.142	0.1412	0.14	0.1577	0.16	RANDOM	15.229

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
r_dihedral_angle_2_deg	28.445
r_dihedral_angle_4_deg	14.013
r_dihedral_angle_3_deg	13.03
r_dihedral_angle_1_deg	6.205
r_angle_other_deg	2.328
r_angle_refined_deg	2.076
r_chiral_restr	0.117
r_bond_refined_d	0.018
r_gen_planes_refined	0.018
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	437
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	31

Software

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