5LU4 | pdb_00005lu4

C4-type pyruvate phosphate dikinase: conformational intermediate of 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	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 (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	109.79	46418	2229	99.61	0.2492	0.2474	0.24	0.2864	0.28	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.