4LSM | pdb_00004lsm

Crystal structure of a glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	TrcrA.00814.b.B1.PS01922 at 29.1 mg/mL against JCSG+ screen condition G8 (0.15 M DL-malic acid, 25% PEG3350), cryoprotectant: 15% ethylene glycol, crystal tracking ID 246268g8, unique puck ID roi5-9, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.49	α = 90
b = 80.49	β = 90
c = 203.06	γ = 120

Symmetry
Space Group	P 32 2 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	RAYONIX MX-300		2012-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.65	50	99.9	0.092	16.1	10.3	92667	92582		-3	25.482

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	1.65	1.69	100		0.434	5.06

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 1GAD	1.65	48.61	92504	4627	99.92	0.1337	0.1317	0.15	0.1702	0.18	RANDOM	22.6967

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]
0.14	0.14		0.14		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.272
r_sphericity_free	29.029
r_dihedral_angle_4_deg	16.339
r_dihedral_angle_3_deg	12.165
r_sphericity_bonded	7.039
r_dihedral_angle_1_deg	6.341
r_rigid_bond_restr	2.23
r_mcangle_it	1.766
r_angle_refined_deg	1.396
r_mcbond_other	1.357

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.272
r_sphericity_free	29.029
r_dihedral_angle_4_deg	16.339
r_dihedral_angle_3_deg	12.165
r_sphericity_bonded	7.039
r_dihedral_angle_1_deg	6.341
r_rigid_bond_restr	2.23
r_mcangle_it	1.766
r_angle_refined_deg	1.396
r_mcbond_other	1.357
r_mcbond_it	1.356
r_angle_other_deg	0.778
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4934
Nucleic Acid Atoms
Solvent Atoms	645
Heterogen Atoms	112

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.