2X0S | pdb_00002x0s

3.0 A RESOLUTION CRYSTAL STRUCTURE OF GLYCOSOMAL PYRUVATE PHOSPHATE DIKINASE FROM TRYPANOSOMA BRUCEI

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.8		HANGING DROP, 2 MICROLITER PROTEIN AND 2 MICROLITER PRECIPITANT SOLUTION. PROTEIN SOLUTION. 50 MG/ML, 20 MM IMIDAZOLE PH 7.0, 100 MM NACL, 100 MM MGCL2, 20% (V/V) GLYCEROL. PRECIPITANT SOLUTION. 0.1 M BICINE PH 8.8, 1.5 % (W/V) PEG 5000 MONOMETHYLETHER, 10 % (V/V) GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
3.1	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.17	α = 90
b = 153.5	β = 90
c = 65.46	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	277	IMAGE PLATE	MARRESEARCH		2000-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LURE BEAMLINE DW32		LURE	DW32

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	24	96	0.09	14.8	5.3		24120			61

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	3	3.1	88.6		0.28	3.1	3.4

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 1DIK	2.997	23.938	1.62	24115	1163	95.73	0.1687	0.1649	0.17	0.2415	0.24	81.08

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]
6.1816			-1.6729		-4.8838

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.423
f_angle_d	1.345
f_chiral_restr	0.082
f_bond_d	0.009
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6935
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
BIOMOL	data scaling
CNS	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.