4JA8 | pdb_00004ja8

Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with AGI-6780 Inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	298	Crystals of the IDH2/R140Q:AGI-6780 complex were grown by hanging drop vapor diffusion at 18C after mixing the IDH2/R140Q:AGI-6780 sample with a 2 to 1 volume of protein to reservoir solution. Reservoir solution was comprised of 0.2 M Calcium chloride, 0.1 M TRIS (pH 8.5) and 25 % w/v PEG 4000. Seeding methods were used to grow diffraction quality crystals, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.656	α = 90
b = 119.661	β = 90
c = 125.542	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	1.5418	APS	21-ID-G

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	1.55	50	99.8	0.054	13.9	6.7		128343

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	1.55	1.61	98.8		0.422		4.9	12522

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.55	31.9	127987	6429	99.51	0.1834	0.1816	0.18	0.2179	0.22	RANDOM	21.3273

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]
-0.01					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.082
r_dihedral_angle_4_deg	18.28
r_dihedral_angle_3_deg	14.552
r_dihedral_angle_1_deg	6.217
r_scangle_it	4.721
r_scbond_it	3.187
r_angle_refined_deg	2.145
r_mcangle_it	2.1
r_mcbond_it	1.3
r_chiral_restr	0.285

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.082
r_dihedral_angle_4_deg	18.28
r_dihedral_angle_3_deg	14.552
r_dihedral_angle_1_deg	6.217
r_scangle_it	4.721
r_scbond_it	3.187
r_angle_refined_deg	2.145
r_mcangle_it	2.1
r_mcbond_it	1.3
r_chiral_restr	0.285
r_bond_refined_d	0.028
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6537
Nucleic Acid Atoms
Solvent Atoms	746
Heterogen Atoms	154

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	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.