3K2H

Co-crystal structure of dihydrofolate reductase/thymidylate synthase from Babesia bovis with dUMP, Pemetrexed and NADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I3R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	289	11.3 mg/mL BaboA.01191.a, 2 mM dUMP, 2 mM Pemetrexed, NADP carried through from protein purification so it could be NADP or NADPH; soak of apo crystals grown in 20% PEG 8000, 0.1 M CHES pH 9.5; crystal tracking ID 204850f1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.144	α = 119.69
b = 83.196	β = 90.85
c = 83.378	γ = 101.71

Symmetry
Space Group	P 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	RIGAKU SATURN 944+		2009-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.2	50	98.5	0.096	15.4	4		58064

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	2.2	2.24	82.6		0.286	3.16	2.7	2401

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	3i3r	2.2	35.2	57443	2917	97.03	0.192	0.19	0.239	RANDOM	16.674

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]
1.4	0.6	0.21	-0.06	0.78	-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.686
r_dihedral_angle_4_deg	21.604
r_dihedral_angle_3_deg	14.171
r_dihedral_angle_1_deg	6.556
r_scangle_it	2.851
r_scbond_it	1.933
r_angle_refined_deg	1.507
r_mcangle_it	1.17
r_mcbond_it	0.654
r_chiral_restr	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.686
r_dihedral_angle_4_deg	21.604
r_dihedral_angle_3_deg	14.171
r_dihedral_angle_1_deg	6.556
r_scangle_it	2.851
r_scbond_it	1.933
r_angle_refined_deg	1.507
r_mcangle_it	1.17
r_mcbond_it	0.654
r_chiral_restr	0.109
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8001
Nucleic Acid Atoms
Solvent Atoms	727
Heterogen Atoms	280

Software

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

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.