8E90

Inhibition of Human Menin by SNDX-5613

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.9	294	0.1M HEPES pH 7.9, 24%(w/v) PEG 3350, 0.2M Magnesium nitrate, 20%(v/v) Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.417	α = 90
b = 86.134	β = 90
c = 202.027	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 EIGER X 16M		2021-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953644	Australian Synchrotron	MX2

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	1.85	48.39	99.93	0.121	0.163	0.116	0.994	6.2	3.8		87900			37.82

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	1.85	1.898	99.97		1.43	1.67	1.13	0.27	0.8	3.4

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6PKC	1.85	48.3	87900	4385	99.932	0.174	0.174	0.1726	0.2098	Random	29.349

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]
0.002			-0.001		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.526
r_dihedral_angle_4_deg	15.546
r_dihedral_angle_3_deg	14.202
r_dihedral_angle_1_deg	9.016
r_lrange_it	6.506
r_lrange_other	6.462
r_scangle_it	5.17
r_scangle_other	5.17
r_mcangle_it	3.606
r_mcangle_other	3.605
r_scbond_it	3.425
r_scbond_other	3.425
r_mcbond_it	2.566
r_mcbond_other	2.565
r_angle_refined_deg	1.598
r_chiral_restr_other	1.564
r_angle_other_deg	1.513
r_nbd_refined	0.232
r_xyhbond_nbd_other	0.195
r_nbd_other	0.19
r_xyhbond_nbd_refined	0.183
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.167
r_symmetry_nbd_refined	0.166
r_symmetry_xyhbond_nbd_other	0.122
r_ncsr_local_group_1	0.101
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7282
Nucleic Acid Atoms
Solvent Atoms	520
Heterogen Atoms	116

Software

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