6BM7 | pdb_00006bm7

Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodimer in complex with pyrimidineamine inhibitor UTSAM568

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TVM	PDB entry 5TVM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	1 uL 4 mg/mL protein in crystallization buffer (50 mM Bis-Tris propane, pH 7.2, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine, 0.5 mM N4-(3,5-dibromophenyl)-6-methylpyrimidine-2,4-diamine [UTSAM568], 1% DMSO) + 1 uL reservoir solution (17% PEG6000, 100 mM Bis-Tris propane, pH 7.0) + 0.5 uL unliganded protein microseeds obtained using Seed-Bead method in stabilization solution (100 mM Bis-Tris propane, pH 8.9, 50 mM HEPES, pH 7.2, 19% PEG6000, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine)

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.09	α = 90
b = 96.25	β = 102.426
c = 98.84	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	ADSC QUANTUM 315r		2015-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.91905	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	2.98	50	99.8	0.194	0.074	10	6.8		30294			49.2238648407

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.05	99.1		0.712	1.87	6.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	FREE R-VALUE	PDB entry 5TVM	2.98	48.2623233532	1.33789805147	50644	2520	84.6026628356	0.202335356515	0.199589623624	0.2	0.254857270037	0.25	58.4151476361

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.4170911814
f_angle_d	0.558602768216
f_chiral_restr	0.0446252615216
f_plane_restr	0.00364942909324
f_bond_d	0.00314584829052

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10193
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	117

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	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.