5AQ1 | pdb_00005aq1

Trypanosoma cruzi Glucose-6-phosphate Dehydrogenase in complex with G6P and NADPH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4E9I	PDB ENTRY 4E9I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				PROTEIN: 2UL TCG6PD 10MG/ML, 5MM G6P, 2 MM NADPH; BUFFER: 20 MM TRIS PH 8.0 WITH 0.2 M NACL AND 5 MM ME PRECIPITANT: 1 UL JEFFAMINE ED-2003 PH 7.0 30%, 0.1 M HEPES PH 7.0;

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.946	α = 90
b = 154.946	β = 90
c = 348.358	γ = 90

Symmetry
Space Group	I 41 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2015-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1		Diamond	I04-1

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	2.65	49.13	95.4	0.12	11.1	8.7		58510		2.5	39.6

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	2.65	2.72	96.9		0.79	2.5	8.6

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 4E9I	2.65	141.57	55569	2941	94.73	0.20118	0.19991	0.21	0.22553	0.23	RANDOM	47.798

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]
0.96			0.96		-1.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.93
r_dihedral_angle_4_deg	16.075
r_dihedral_angle_3_deg	15.113
r_dihedral_angle_1_deg	5.532
r_mcangle_it	2.725
r_scbond_it	1.804
r_mcbond_it	1.544
r_mcbond_other	1.544
r_angle_refined_deg	1.048
r_angle_other_deg	0.808
r_chiral_restr	0.056
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11571
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	192

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing