9M6P | pdb_00009m6p

Discovery of a bifunctional PKMYT1-targeting PROTAC empowered by AI-generation

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8D6E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	SM5-E1+30%Gly

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.927	α = 90
b = 127.927	β = 90
c = 184.655	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	298	PIXEL	DECTRIS EIGER X 16M		2022-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97626	Diamond	I03

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	1.88	100	100	0.168	10	13		24659

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	1.88	1.92			1.213

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.383	95.001	12839	652	54.688	0.207	0.2028	0.2056	0.2898	0.29	RANDOM	62.015

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]
0.028	0.014		0.028		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.633
r_dihedral_angle_3_deg	18.147
r_dihedral_angle_4_deg	17.817
r_lrange_it	9.214
r_lrange_other	9.214
r_dihedral_angle_1_deg	7.208
r_mcangle_other	6.105
r_mcangle_it	6.103
r_scangle_other	6.067
r_scangle_it	6.064
r_mcbond_it	3.771
r_mcbond_other	3.754
r_scbond_it	3.688
r_scbond_other	3.681
r_angle_refined_deg	1.345
r_angle_other_deg	1.132
r_symmetry_xyhbond_nbd_refined	0.267
r_nbd_refined	0.225
r_nbd_other	0.224
r_symmetry_nbd_other	0.189
r_symmetry_nbd_refined	0.177
r_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.163
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.049
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4341
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	61

Software

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