4AJR

3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, magnesium(II) and NADPH - The product complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AI2	PDB ENTRY 1AI2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				1.85 M NH4SO4, 50 MM CITRIC ACID/NA2HPO4 BUFFER PH 5.2, 0.1 M NACL AND 0.2 M DTT

Crystal Properties
Matthews coefficient	Solvent content
4.5	72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.788	α = 90
b = 105.788	β = 90
c = 145.488	γ = 90

Symmetry
Space Group	P 43 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	100	CCD	ADSC QUANTUM 315r	TOROIDAL MIRROR		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.69	60	99.5	0.12	15.2	8.6		23556		-3	47.08

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	2.69	2.85	97.5		0.84	2.8	8.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1AI2	2.687	52.894	1.99	23554	1195	99.51	0.1628	0.1604	0.2091

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]
22.8121			22.8121		13.9255

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.288
f_angle_d	1.139
f_chiral_restr	0.069
f_bond_d	0.008
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3204
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	81

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	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.