3DAT | pdb_00003dat

Crystal structure of the ternary MTX NADPH complex of Bacillus anthracis dihydrofolate reductase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QK8	PDB entry 2QK8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277	0.1 M Bis-Tris pH 5.5, 0.2 M CaCl2, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.9	α = 90
b = 43.156	β = 119.31
c = 67.87	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	MAR CCD 165 mm	Mirrors	2008-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	0.90000	APS	14-ID-B

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	2.1	20	93.8	0.131	8.6	3.1		10216	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.17	73.3		0.286	3	1.9	823

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 2QK8	2.3	15.31	1	1	8332	8170	404	91.92	0.239	0.237	0.24	0.277	0.27	RANDOM	44.502

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]
-0.03		-0.21	0.14		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.816
r_dihedral_angle_3_deg	21.993
r_dihedral_angle_4_deg	17.853
r_dihedral_angle_1_deg	8.102
r_scangle_it	2.87
r_angle_refined_deg	1.892
r_scbond_it	1.856
r_mcangle_it	1.234
r_mcbond_it	0.759
r_nbtor_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.816
r_dihedral_angle_3_deg	21.993
r_dihedral_angle_4_deg	17.853
r_dihedral_angle_1_deg	8.102
r_scangle_it	2.87
r_angle_refined_deg	1.892
r_scbond_it	1.856
r_mcangle_it	1.234
r_mcbond_it	0.759
r_nbtor_refined	0.323
r_nbd_refined	0.24
r_symmetry_hbond_refined	0.201
r_xyhbond_nbd_refined	0.178
r_symmetry_vdw_refined	0.165
r_chiral_restr	0.126
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1280
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	81

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BioCARS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
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 R01GM157729.