9E5F | pdb_00009e5f

Discovery of an Orally Bioavailable KRAS G12D Inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Sodium acetate, pH 4.6,30% PEG 4000 and 0.2M ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.175	α = 90
b = 53.63	β = 90
c = 90.206	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	100	PIXEL	DECTRIS PILATUS 6M		2020-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.35	53.63	99.5	0.04	0.04	0.01	1	26.4	12.6		43420			12.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.37	95.4		0.3	0.32	0.1	0.96	3.7	9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.35	46.099	43359	2120	99.404	0.155	0.1535	0.1614	0.1782	0.1816	18.98

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]
-0.038			-0.598		0.636

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.85
r_dihedral_angle_6_deg	16.356
r_lrange_it	12.6
r_lrange_other	11.988
r_dihedral_angle_3_deg	11.536
r_dihedral_angle_other_2_deg	7.628
r_scangle_it	6.462
r_scangle_other	6.46
r_dihedral_angle_1_deg	5.968
r_mcangle_it	4.722
r_mcangle_other	4.72
r_scbond_it	4.508
r_scbond_other	4.506
r_rigid_bond_restr	4.052
r_mcbond_it	3.077
r_mcbond_other	3.076
r_angle_refined_deg	2.007
r_angle_other_deg	1.104
r_nbd_other	0.216
r_nbd_refined	0.213
r_symmetry_nbd_refined	0.174
r_nbtor_refined	0.173
r_symmetry_nbd_other	0.148
r_chiral_restr	0.115
r_symmetry_xyhbond_nbd_refined	0.115
r_xyhbond_nbd_refined	0.104
r_symmetry_nbtor_other	0.069
r_gen_planes_refined	0.016
r_bond_refined_d	0.012
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1371
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing