3LCB

The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	295	25% PEG 300, 0.1M MES, 0.05M magnesium chloride, 0.002M DTT,10% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.85	68.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 196.801	α = 90
b = 196.801	β = 90
c = 156.458	γ = 120

Symmetry
Space Group	P 63

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 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.9879	CHESS	A1

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	2.9	30	99.3	0.114	21.8	14.9	75640	38980

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)
	2.9	3	99.4		0.572	1.4	14	3863

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.9	30	3778	98.15	0.192	0.19	0.222	RANDOM	71.363

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]
-3.82			-3.82		7.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.98
r_dihedral_angle_3_deg	19.494
r_dihedral_angle_4_deg	17.851
r_dihedral_angle_1_deg	5.387
r_scangle_it	1.755
r_mcangle_it	1.294
r_angle_refined_deg	1.139
r_scbond_it	1.02
r_mcbond_it	0.718
r_rigid_bond_restr	0.657

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.98
r_dihedral_angle_3_deg	19.494
r_dihedral_angle_4_deg	17.851
r_dihedral_angle_1_deg	5.387
r_scangle_it	1.755
r_mcangle_it	1.294
r_angle_refined_deg	1.139
r_scbond_it	1.02
r_mcbond_it	0.718
r_rigid_bond_restr	0.657
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15640
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	110

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.