3JQA | pdb_00003jqa

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-1,9-dihydro-6H-purine-6-thione (DX4)

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
2.07	40.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.997	α = 90
b = 90.834	β = 115.5
c = 82.64	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	2006-05-21		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	1.9	57.64	99.9	0.057	0.057	9.9	3		78741

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	1.9	2	99.9		0.32	0.32	2.1	3.3	11433

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	1.9	57.64	78702	3960	99.87	0.149	0.147	0.16	0.189	0.2	RANDOM	23.802

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]
-1.22		-0.54	1.63		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.73
r_dihedral_angle_4_deg	16.781
r_dihedral_angle_3_deg	13.448
r_dihedral_angle_1_deg	5.566
r_scangle_it	5.252
r_scbond_it	4.05
r_mcangle_it	2.828
r_mcbond_it	2.418
r_angle_refined_deg	1.342
r_angle_other_deg	0.937
r_mcbond_other	0.638
r_symmetry_hbond_refined	0.239
r_symmetry_vdw_other	0.232
r_nbd_refined	0.196
r_nbd_other	0.182
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.155
r_symmetry_vdw_refined	0.124
r_nbtor_other	0.084
r_chiral_restr	0.073
r_xyhbond_nbd_other	0.021
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7414
Nucleic Acid Atoms
Solvent Atoms	638
Heterogen Atoms	236

Software

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