7B0T | pdb_00007b0t

Crystal structure of MLLT1 YEATS domain T3 mutant in complex with benzimidazole-amide based compound 1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6T1J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	28% PEG 3350, 0.2M NaOAc, 0.1M Bis-Tris, pH6.0

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.739	α = 90
b = 48.739	β = 90
c = 131.995	γ = 90

Symmetry
Space Group	P 43 21 2

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		2020-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000	SLS	X06SA

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	2.05	48.74	100	0.094	0.099	0.031	0.999	11.5	9.6		10697

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.11	100		1.169	0.378	0.858		10.1

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 (Observed)	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	6t1j	2.05	45.72	10142	496	99.95	0.2208	0.218	0.22	0.2756	0.28	RANDOM	56.281

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]
-2.7			-2.7		5.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	21.987
r_dihedral_angle_2_deg	20.477
r_dihedral_angle_3_deg	16.091
r_dihedral_angle_1_deg	7.861
r_angle_refined_deg	1.313
r_angle_other_deg	1.177
r_chiral_restr	0.064
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	21.987
r_dihedral_angle_2_deg	20.477
r_dihedral_angle_3_deg	16.091
r_dihedral_angle_1_deg	7.861
r_angle_refined_deg	1.313
r_angle_other_deg	1.177
r_chiral_restr	0.064
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1123
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	47

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MLPHARE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.