6T1I | pdb_00006t1i

Crystal structure of MLLT1 (ENL) YEATS domain in complexed with piperazine-urea derivative 1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HQ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	25% PEG 3350, 0.2 M sodium chloride, 0.1 M bis-tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.936	α = 90
b = 48.936	β = 90
c = 132.776	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		2018-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0000	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	1.8	48.94	100	0.071	0.078	0.025	0.999	13.7	9.6		15758			35.4

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	1.8	1.86	100		0.806	0.891	0.278	0.891	2.2	9.9

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	6HQ0	1.8	45.92	14935	783	99.94	0.2065	0.2051	0.21	0.2322	0.23	RANDOM	44.694

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]
-2.13			-2.13		4.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.407
r_dihedral_angle_4_deg	17.873
r_dihedral_angle_3_deg	12.534
r_dihedral_angle_1_deg	7.165
r_angle_refined_deg	1.332
r_angle_other_deg	1.227
r_chiral_restr	0.068
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.407
r_dihedral_angle_4_deg	17.873
r_dihedral_angle_3_deg	12.534
r_dihedral_angle_1_deg	7.165
r_angle_refined_deg	1.332
r_angle_other_deg	1.227
r_chiral_restr	0.068
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1182
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	71

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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.