8VA6 | pdb_00008va6

Menin 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	7.5	277	0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.395	α = 90
b = 80.181	β = 90
c = 124.924	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		2016-06-07	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	1.57	50	100	0.072	33.4	6.9		68768

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	1.57	1.6	100		0.772	2.13	6.3

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	1.57	41.467	68695	3434	99.952	0.16	0.1581	0.1592	0.1933	0.1941	23.252

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]
1.513			0.053		-1.566

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.077
r_dihedral_angle_3_deg	12.183
r_dihedral_angle_2_deg	9.052
r_lrange_it	6.978
r_lrange_other	6.977
r_dihedral_angle_1_deg	6.13
r_scangle_it	5.536
r_scangle_other	5.535
r_dihedral_angle_other_2_deg	4.733
r_scbond_it	3.729
r_scbond_other	3.728
r_mcangle_other	3.663
r_mcangle_it	3.662
r_mcbond_it	2.467
r_mcbond_other	2.467
r_angle_refined_deg	1.825
r_angle_other_deg	0.648
r_symmetry_xyhbond_nbd_refined	0.279
r_symmetry_nbd_refined	0.239
r_nbd_refined	0.222
r_nbd_other	0.186
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_chiral_restr_other	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3670
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	116

Software

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