2QK8

Crystal structure of the anthrax drug target, Bacillus anthracis dihydrofolate reductase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZDR	PDB ENTRY: 1ZDR (Bacillus stearothermophilus DHFR)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.1 M Bis-Tris pH 5.5, 0.2 M CaCl2, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.697	α = 90
b = 41.236	β = 119.2
c = 67.032	γ = 90

Symmetry
Space Group	C 1 2 1

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	ADSC QUANTUM 315	Bent conical Si-mirror (Rh coated) Bent Ge(111) monochromator	2006-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	58.4	92.3	0.099	13.7	3.3	16860	10104		2	32.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	76.8		0.342	2.8	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	PDB ENTRY: 1ZDR (Bacillus stearothermophilus DHFR)	2.4	22	2.8	7545	7171	374	95.68	0.24422	0.24273	0.27382	RANDOM	44.402

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	38.162
r_dihedral_angle_4_deg	22.184
r_dihedral_angle_3_deg	21.543
r_dihedral_angle_1_deg	9.67
r_scangle_it	3.155
r_scbond_it	2.167
r_angle_refined_deg	1.895
r_mcangle_it	1.725
r_mcbond_it	0.959
r_nbtor_refined	0.335

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.162
r_dihedral_angle_4_deg	22.184
r_dihedral_angle_3_deg	21.543
r_dihedral_angle_1_deg	9.67
r_scangle_it	3.155
r_scbond_it	2.167
r_angle_refined_deg	1.895
r_mcangle_it	1.725
r_mcbond_it	0.959
r_nbtor_refined	0.335
r_nbd_refined	0.281
r_symmetry_vdw_refined	0.269
r_symmetry_hbond_refined	0.214
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.123
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1347
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
BioCARS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	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 R01GM157729.