3DOC

Crystal Structure of TrkA glyceraldehyde-3-phosphate dehydrogenase from Brucella melitensis

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	289	JCSG+ screen well B2, 20% PEG 3350, 0.2 M sodium isothiocyanate, , pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.975	α = 90
b = 106.333	β = 107.89
c = 90.776	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	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

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	2.4	50	97.8	0.15	11.6	3.5		49106

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)
	2.4	2.49	98.4		0.444	2.4	3.5	4907

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1OBF	2.4	50	49077	2471	96.91	0.187	0.185	0.225	RANDOM	22.613

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]
0.44		0.02	0.24		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.003
r_dihedral_angle_4_deg	19.712
r_dihedral_angle_3_deg	19.308
r_dihedral_angle_1_deg	6.232
r_scangle_it	2.561
r_scbond_it	1.578
r_angle_refined_deg	1.467
r_mcangle_it	0.998
r_mcbond_it	0.524
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.003
r_dihedral_angle_4_deg	19.712
r_dihedral_angle_3_deg	19.308
r_dihedral_angle_1_deg	6.232
r_scangle_it	2.561
r_scbond_it	1.578
r_angle_refined_deg	1.467
r_mcangle_it	0.998
r_mcbond_it	0.524
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10164
Nucleic Acid Atoms
Solvent Atoms	521
Heterogen Atoms	176

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.