5LU4

C4-type pyruvate phosphate dikinase: conformational intermediate of central domain in the swiveling mechanism

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	285.15	0.1 M MES (pH 6.5), 0.3 M MgCl2, 10% (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.159	α = 90
b = 126.515	β = 90
c = 218.998	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F	KB mirrors	2016-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9686	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.9	219	99.8	0.047	0.999	20.1	4.9		46486

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	99.7		0.499	0.871		5.2

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	5JVL	2.9	109.79	46418	2229	99.61	0.2492	0.2474	0.2864	RANDOM	99.0676

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]
4.41			-0.64		-3.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.413
r_dihedral_angle_4_deg	13.251
r_dihedral_angle_3_deg	11.319
r_dihedral_angle_1_deg	5.616
r_angle_other_deg	3.933
r_angle_refined_deg	1.528
r_mcangle_it	0.553
r_mcbond_it	0.307
r_mcbond_other	0.307
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.413
r_dihedral_angle_4_deg	13.251
r_dihedral_angle_3_deg	11.319
r_dihedral_angle_1_deg	5.616
r_angle_other_deg	3.933
r_angle_refined_deg	1.528
r_mcangle_it	0.553
r_mcbond_it	0.307
r_mcbond_other	0.307
r_chiral_restr	0.082
r_bond_refined_d	0.017
r_gen_planes_other	0.012
r_gen_planes_refined	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11954
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	64

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUCCANEER	model building
REFMAC	refinement
PHENIX	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 R01GM133198.