9TBR | pdb_00009tbr

From KRASG12D to pan-KRAS inhibitors

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	0.1M NaH2PO4/Na2HPO4 pH 9, 30.0% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.683	α = 90
b = 94.683	β = 90
c = 120.648	γ = 120

Symmetry
Space Group	H 3 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	PIXEL	DECTRIS EIGER2 R 1M		2020-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.6	40.25	93.4	0.079	23.04	10		27746

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.759			0.59	1.1

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	FOURIER SYNTHESIS	THROUGHOUT	1.65	40.25	20419	1053	84.33	0.17849	0.17664	0.1875	0.21214	0.2233	RANDOM	32.538

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]
0.17	0.08		0.17		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.235
r_dihedral_angle_3_deg	16.255
r_dihedral_angle_4_deg	13.788
r_dihedral_angle_1_deg	11.563
r_long_range_B_refined	5.859
r_long_range_B_other	5.808
r_scbond_it	2.616
r_scbond_other	2.614
r_mcbond_it	1.926
r_mcbond_other	1.925
r_angle_refined_deg	1.455
r_angle_other_deg	0.488
r_chiral_restr	0.06
r_bond_refined_d	0.01
r_bond_other_d	0.002
r_gen_planes_refined	0.001
r_gen_planes_other
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_mcangle_it
r_mcangle_other
r_scangle_it
r_scangle_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1358
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
REFMAC	phasing