5LGE | pdb_00005lge

Crystal Structure of human IDH1 mutant (R132H) in complex with NADP+ and an Inhibitor related to BAY 1436032

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KZO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	PROTEIN BUFFER: 15 MG/ML. PROTEIN IN 25 MM HEPES, 300 MM NACL, 5 MM BETA-ME, COMPLETE PROTEASE INHIBITOR MIXTURE, PH 7.7 RESERVOIR: 100 MM BIS-TRIS, PH 7.0, 200 MM CA-ACETATE, 20.0 %(W/V) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.9	α = 90
b = 110.32	β = 91.19
c = 198.54	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS PILATUS 6M-F		2013-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

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	2.7	30	98.7	0.12	8.6	4.8		56625		2

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	2.7	2.85	99		0.7	2.3	4.8

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	4KZO	2.7	29.94	53784	2839	98.53	0.19722	0.19546	0.2	0.22977	0.23	RANDOM	73.2

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]
-0.03		0.48	-0.43		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.606
r_dihedral_angle_4_deg	20.556
r_dihedral_angle_3_deg	17.938
r_dihedral_angle_1_deg	6.319
r_long_range_B_refined	5.967
r_long_range_B_other	5.89
r_mcangle_it	2.718
r_mcangle_other	2.718
r_scangle_other	2.571
r_mcbond_it	1.532
r_mcbond_other	1.532
r_angle_refined_deg	1.484
r_scbond_it	1.454
r_scbond_other	1.454
r_angle_other_deg	1.317
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12995
Nucleic Acid Atoms
Solvent Atoms	511
Heterogen Atoms	270

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing