5JVN | pdb_00005jvn

C3-type pyruvate phosphate dikinase: intermediate state of the central domain in the swiveling mechanism

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	285.15	17 % (w/v) PEG 4000, 15 % (w/v) glycerol, 85 mM HEPES (pH 7.5), 5 % (v/v) isopropanol, 10 mM phosphoenol pyruvate, 2.5 mM magnesium sulfate, 1 mM 2'-Br-dAppNHp

Crystal Properties
Matthews coefficient	Solvent content
4	68.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 249.43	α = 90
b = 249.43	β = 90
c = 84.06	γ = 120

Symmetry
Space Group	P 6 2 2

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 PILATUS3 6M	Toroidal mirror	2015-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976252	ESRF	ID29

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	49.54	99.9	0.089	0.999	13.9	6.9		34537			65.68

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	2.9	3.04	100		0.597	2.7	6.8

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	5JVL	2.9	49.54	34536	1695	99.87	0.1996	0.1978	0.2	0.2352	0.23	RANDOM	90.5836

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]
1.68	0.84		1.68		-5.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.861
r_dihedral_angle_4_deg	15.835
r_dihedral_angle_3_deg	14.07
r_dihedral_angle_1_deg	4.788
r_angle_other_deg	3.682
r_mcangle_it	3.084
r_mcbond_it	1.933
r_mcbond_other	1.93
r_angle_refined_deg	1.149
r_chiral_restr	0.054

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.861
r_dihedral_angle_4_deg	15.835
r_dihedral_angle_3_deg	14.07
r_dihedral_angle_1_deg	4.788
r_angle_other_deg	3.682
r_mcangle_it	3.084
r_mcbond_it	1.933
r_mcbond_other	1.93
r_angle_refined_deg	1.149
r_chiral_restr	0.054
r_bond_refined_d	0.01
r_gen_planes_other	0.005
r_gen_planes_refined	0.004
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6496
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	42

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUCCANEER	model building
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.