3JQ6

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6,7-bis(1-methylethyl)pteridine-2,4-diamine (DX1)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C7V	PDB entry 2C7V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	2-3M Sodium acetate, 10-100mM Sodium citrate, pH 4.0-6.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.141	α = 90
b = 89.468	β = 115.48
c = 84.342	γ = 90

Symmetry
Space Group	P 1 21 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 315r	Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror	2005-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97550	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	30.66	99.9	0.08	0.08	13.5	4.3		92014

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	100		0.364	0.364	1.9	4.3	13424

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	PDB entry 2C7V	1.8	30.66	91988	4650	99.91	0.152	0.15	0.19	RANDOM	17.935

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]
-1.52		-0.51	2.99		-1.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.104
r_dihedral_angle_4_deg	19.346
r_dihedral_angle_3_deg	14.184
r_dihedral_angle_1_deg	5.597
r_scangle_it	4.93
r_scbond_it	3.719
r_mcangle_it	2.516
r_mcbond_it	1.791
r_angle_refined_deg	1.305
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.104
r_dihedral_angle_4_deg	19.346
r_dihedral_angle_3_deg	14.184
r_dihedral_angle_1_deg	5.597
r_scangle_it	4.93
r_scbond_it	3.719
r_mcangle_it	2.516
r_mcbond_it	1.791
r_angle_refined_deg	1.305
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.23
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.186
r_symmetry_hbond_refined	0.183
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7397
Nucleic Acid Atoms
Solvent Atoms	1023
Heterogen Atoms	296

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	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.