Experiment: 9YLL

BCL11A ZF4-6 in Complex with a DNA Sequence Observed in the Human Globin Locus Containing Motif TGTCCA (20-mer)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9E6R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	292	20% w/v Polyethylene glycol 3,350 0.2M sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
4.49	72.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.861	α = 90
b = 58.861	β = 90
c = 256.31	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 9M		2024-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.92026	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.38	34.9	46.5	0.154	0.032	0.998	13.7	24.7		15340			48.07

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.38	2.76			0.478	0.646

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.38	34.9	1.33	15340	753	44.47	0.2073	0.2053	0.206	0.247	0.2476	74.71

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	25.8473
f_angle_d	0.5312
f_chiral_restr	0.0313
f_bond_d	0.0032
f_plane_restr	0.0015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	668
Nucleic Acid Atoms	814
Solvent Atoms	7
Heterogen Atoms	3

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHENIX	phasing