3JQD

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-4-oxo-6-phenyl-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (DX7)

X-RAY DIFFRACTION

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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
2.11	41.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.641	α = 90
b = 90.731	β = 115.33
c = 84.636	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 325 mm CCD	Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry	2005-05-20	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)	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	1.6	38.98	81.7	0.089	0.089	10.2	3.1		108123

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	1.6	1.69	84.9		0.332	0.332	2.2	2.9	16413

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	1.6	38.4	108063	5434	80.7	0.181	0.179	0.216	RANDOM	16.228

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]
-0.73		-0.3	1.58		-1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.552
r_dihedral_angle_4_deg	14.589
r_dihedral_angle_3_deg	12.036
r_dihedral_angle_1_deg	5.261
r_scangle_it	3.357
r_scbond_it	2.544
r_mcangle_it	1.697
r_mcbond_it	1.406
r_angle_refined_deg	1.154
r_angle_other_deg	0.846
r_mcbond_other	0.383
r_nbd_refined	0.191
r_symmetry_vdw_other	0.184
r_nbd_other	0.174
r_nbtor_refined	0.166
r_symmetry_vdw_refined	0.131
r_symmetry_hbond_refined	0.128
r_xyhbond_nbd_refined	0.105
r_nbtor_other	0.081
r_chiral_restr	0.057
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7404
Nucleic Acid Atoms
Solvent Atoms	1196
Heterogen Atoms	272

Software

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