3NRR | pdb_00003nrr

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K2H	PDB ENTRY 3K2H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	1:1 CO-CRYSTALLIZATION DROP. PROTEIN SOLUTION: 20 MG/ML PROTEIN, 2.0MM DUMP, 2.0MM NADP, 5.0MM RALTITREXED, 0.5M SODIUM CHLORIDE, 0.025M HEPES, 5%(V/V) GLYCEROL, 2.0MM DITHIOTHREITOL. CRYSTALLANT SOLUTION (HT INDEX E11): 0.02M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1M HEPES, 22%(W/V) POLY(ACRYLIC ACID) SODIUM SALT 5100, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.33	α = 119.61
b = 83.83	β = 102.04
c = 83.92	γ = 90.26

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	ADSC QUANTUM 315		2010-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.99740	ALS	5.0.1

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	1.8	50	97.2	0.06	12.3	2		108796

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	1.8	1.83	95.9		0.354	2.439	2	10489

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3K2H	1.8	19.94	108796	104245	5573	98.52	0.1956	0.1935	0.21	0.236	0.25	RANDOM	19.8103

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]
-1.91	0.06	-0.25	1.5	1.26	1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.942
r_dihedral_angle_4_deg	20.686
r_dihedral_angle_3_deg	12.993
r_dihedral_angle_1_deg	6.392
r_scangle_it	3.202
r_scbond_it	2.129
r_angle_refined_deg	1.753
r_mcangle_it	1.291
r_angle_other_deg	0.982
r_mcbond_it	0.758

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.942
r_dihedral_angle_4_deg	20.686
r_dihedral_angle_3_deg	12.993
r_dihedral_angle_1_deg	6.392
r_scangle_it	3.202
r_scbond_it	2.129
r_angle_refined_deg	1.753
r_mcangle_it	1.291
r_angle_other_deg	0.982
r_mcbond_it	0.758
r_mcbond_other	0.246
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7965
Nucleic Acid Atoms
Solvent Atoms	1025
Heterogen Atoms	329

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
PHASES	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.