8VA5 | pdb_00008va5

Menin mutant - T349M in complex with Ziftomenib (KO-539)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GPQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		285	0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.057	α = 90
b = 80.034	β = 90
c = 124.823	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	CCD	MARMOSAIC 300 mm CCD		2023-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

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	1.3	50	98.9	0.133	24.51	6.6		120002

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	1.3	1.32	96.1		0.981	2.03	4.9

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	THROUGHOUT	1.3	26.344	119911	6193	98.737	0.162	0.1607	0.1617	0.1858	0.1866	13.487

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]
0.728			0.372		-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.414
r_dihedral_angle_2_deg	13.412
r_dihedral_angle_3_deg	11.748
r_dihedral_angle_1_deg	5.858
r_lrange_it	5.49
r_lrange_other	5.489
r_scangle_it	3.93
r_scangle_other	3.929
r_dihedral_angle_other_2_deg	3.923
r_scbond_it	2.595
r_scbond_other	2.594
r_mcangle_it	2.272
r_mcangle_other	2.272
r_angle_refined_deg	2.005
r_mcbond_it	1.517
r_mcbond_other	1.517
r_angle_other_deg	0.682
r_nbd_refined	0.238
r_nbd_other	0.207
r_symmetry_nbd_refined	0.202
r_nbtor_refined	0.186
r_symmetry_nbd_other	0.182
r_symmetry_xyhbond_nbd_refined	0.169
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.105
r_symmetry_xyhbond_nbd_other	0.077
r_symmetry_nbtor_other	0.075
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_chiral_restr_other	0.002
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3667
Nucleic Acid Atoms
Solvent Atoms	634
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing