3JQB | pdb_00003jqb

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-5-(2-phenylethyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one (DX6)

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
2.05	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.671	α = 90
b = 90.433	β = 115.54
c = 82.564	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	2006-05-20		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	2.4	45.22	98.7	0.11	0.11	9.4	2.6		38283

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)
	2.4	2.53	99.2		0.129	0.129	4.2	2.6	5561

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 (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 2C7V	2.4	45.22	38265	1952	98.52	0.195	0.192	0.1913	0.252	0.2477	RANDOM	7.994

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		0.22	1.66		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.698
r_dihedral_angle_4_deg	14.059
r_dihedral_angle_3_deg	14.045
r_dihedral_angle_1_deg	4.934
r_scangle_it	2.508
r_scbond_it	1.739
r_mcangle_it	1.335
r_angle_refined_deg	1.004
r_mcbond_it	0.796
r_nbtor_refined	0.289
r_nbd_refined	0.168
r_symmetry_vdw_refined	0.134
r_xyhbond_nbd_refined	0.111
r_symmetry_hbond_refined	0.105
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7427
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	257

Software

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