8HB9

Crystal Structure of Human IDH1 R132H Mutant in Complex with NADPH and Compound IHMT-IDH1-053

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6B0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		315	24% PEG 3350, 8% Tacsimate pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.759	α = 90
b = 76.426	β = 98.27
c = 171.971	γ = 90

Symmetry
Space Group	P 1 21 1

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 200K		2022-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5406

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	2.8	13.078	99	0.11	8.8	4.1		53443

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	2.8	2.89			0.606

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6b0z	2.8	13.078	53423	2624	98.855	0.218	0.2165	0.2433	41.89

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]
-2.025		0.332	3.625		-1.628

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.821
r_dihedral_angle_4_deg	17.367
r_dihedral_angle_3_deg	14.624
r_dihedral_angle_1_deg	5.679
r_lrange_it	3.928
r_lrange_other	3.909
r_dihedral_angle_other_2_deg	2.94
r_mcangle_it	2.088
r_mcangle_other	2.088
r_chiral_restr_other	1.778
r_scangle_it	1.685
r_scangle_other	1.685
r_angle_refined_deg	1.227
r_angle_other_deg	1.171
r_mcbond_it	1.168
r_mcbond_other	1.166
r_scbond_it	0.913
r_scbond_other	0.913
r_nbd_other	0.198
r_nbd_refined	0.167
r_symmetry_nbd_other	0.15
r_nbtor_refined	0.15
r_xyhbond_nbd_refined	0.128
r_symmetry_nbd_refined	0.126
r_symmetry_xyhbond_nbd_refined	0.104
r_ncsr_local_group_3	0.082
r_symmetry_nbtor_other	0.08
r_ncsr_local_group_5	0.079
r_ncsr_local_group_1	0.075
r_ncsr_local_group_6	0.075
r_ncsr_local_group_2	0.071
r_ncsr_local_group_4	0.07
r_symmetry_xyhbond_nbd_other	0.051
r_chiral_restr	0.037
r_bond_refined_d	0.004
r_bond_other_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12782
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms	269

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing