8XU6 | pdb_00008xu6

Structural Insights into the Tumor Suppressor ZMYND11 Reveal Diverse Recognition Mechanisms

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	40 % v/v 2-Methyl-2,4-pentanediol,100 mM MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.022	α = 90
b = 55.022	β = 90
c = 74.411	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	198	PIXEL	DECTRIS EIGER X 16M		2022-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.9793	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.628	47.76	99.88	0.997	73.4	19		8809

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.66			0.997

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	AB INITIO PHASING	THROUGHOUT	1.628	47.65	8809	430	99.447	0.183	0.1809	0.181	0.2265	0.2266	RANDOM	46.074

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]
1.102	0.551		1.102		-3.576

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.652
r_dihedral_angle_4_deg	16.629
r_dihedral_angle_3_deg	14.94
r_scangle_it	8.428
r_scangle_other	8.424
r_lrange_other	8.061
r_lrange_it	8.033
r_mcangle_it	7.907
r_mcangle_other	7.894
r_scbond_it	7.279
r_scbond_other	7.262
r_dihedral_angle_1_deg	7.106
r_mcbond_it	6.443
r_mcbond_other	6.313
r_rigid_bond_restr	3.707
r_angle_refined_deg	1.561
r_angle_other_deg	0.619
r_symmetry_xyhbond_nbd_refined	0.263
r_symmetry_nbd_other	0.207
r_symmetry_nbd_refined	0.203
r_nbd_refined	0.191
r_nbtor_refined	0.191
r_nbd_other	0.139
r_chiral_restr	0.102
r_xyhbond_nbd_refined	0.094
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	422
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms

Software

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