3GN2 | pdb_00003gn2

Structure of Pteridine Reductase 1 (PTR1) from TRYPANOSOMA BRUCEI in ternary complex with cofactor (NADP+) and inhibitor (DDD00066730)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.5		2-3M SODIUM ACETATE, 10-100MM SODIUM CITRATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.895	α = 90
b = 90.778	β = 115.85
c = 82.861	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					M	SINGLE WAVELENGTH

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

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	67.42	94.9	0.067	0.067	8.3	4.2		124512

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	93.7		0.359	0.359	2	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.6	67.42	124483	6260	94.8	0.148	0.146	0.15	0.178	0.18	13.51

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]
-0.65		-0.37	0.95		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.013
r_dihedral_angle_4_deg	17.396
r_dihedral_angle_3_deg	12.831
r_dihedral_angle_1_deg	5.385
r_scangle_it	4.301
r_scbond_it	3.117
r_mcangle_it	2.194
r_mcbond_it	1.545
r_angle_refined_deg	1.293
r_nbtor_refined	0.304
r_nbd_refined	0.195
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.132
r_symmetry_vdw_refined	0.123
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7400
Nucleic Acid Atoms
Solvent Atoms	1272
Heterogen Atoms	291

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling