2X0N | pdb_00002x0n

Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei determined from Laue data

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GD1	PDB ENTRY 1GD1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		PROTEIN: 5 MICROL OF 6 MG/ML GGAPDH IN 25 MM TRIS HCL PH 7.8, 0.6M AMMONIUM SULPHATE, 2MM NAD, 1MM DITHIOTHREITOL 1MM NA AZIDE, 1 MM EDTA. PRECIPITANT: 5 MICROL OF 52% SATURATED AMMONIUM SULPHATE, 0.2M N,N-BIS-(2-HYDROXYETHYL)-2-AMINOETHANE SULFONIC ACID PH 6.5, 1MM DITHIOTHREITOL, 1MM NA AZIDE, 1MM EDTA, 20MM 3-PHOSPHOGLYCERATE. RESERVOIR: 1 ML

Crystal Properties
Matthews coefficient	Solvent content
4.27	71.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.52	α = 90
b = 256.27	β = 90
c = 114.91	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	273	FILM	CEA			L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.7	0.489-1.905	SRS	PX9.7

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	3.2	7.4	57	0.15	7.2	2.3		34991		1	34.93

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB ENTRY 1GD1	3.2	7.399	2.37	34991	1798	57.28	0.1533	0.1498	0.15	0.2182	0.22	34.75

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]
-4.9115			-0.717		-2.7097

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	22.284
f_angle_d	1.492
f_chiral_restr	0.12
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16410
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	324

Software

Software
Software Name	Purpose
PHENIX	refinement
DARESBURY	data reduction
DARESBURY	data scaling
MERLOT	phasing
BIOMOL	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.