3JQG

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6-[(4-methoxybenzyl)sulfanyl]pyrimidine-2,4-diamine (AX6)

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
2.03	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.531	α = 90
b = 89.845	β = 115.53
c = 82.437	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	MARMOSAIC 225 mm CCD	Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry	2006-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87300	ESRF	ID23-2

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	1.9	53.2	96.5	0.092		2.4		74417

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	1.9	2.01			0.29	1.9	2.7

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	1.9	53.2	74400	3738	96.27	0.214	0.211	0.267	RANDOM	17.855

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]
-2.9		-1.19	3.07		-1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.048
r_dihedral_angle_4_deg	17.36
r_dihedral_angle_3_deg	14.812
r_dihedral_angle_1_deg	5.9
r_scangle_it	4.533
r_scbond_it	3.687
r_mcangle_it	2.497
r_mcbond_it	1.681
r_angle_refined_deg	1.531
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.048
r_dihedral_angle_4_deg	17.36
r_dihedral_angle_3_deg	14.812
r_dihedral_angle_1_deg	5.9
r_scangle_it	4.533
r_scbond_it	3.687
r_mcangle_it	2.497
r_mcbond_it	1.681
r_angle_refined_deg	1.531
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.262
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.201
r_symmetry_hbond_refined	0.181
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7406
Nucleic Acid Atoms
Solvent Atoms	612
Heterogen Atoms	264

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

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.