Experiment: 7LZQ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R28

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Protein (Bcl6 BTB domain(1-129) 13 mg/ml in protein buffer( 20 mM Tris pH 8.3, 300 mM NaCl, 10% glycerol, 1 mM TECEP)) was mixed 1:1 with reservoir buffer (1.3M sodium formate, 0.1M Na acetate pH 5.2. Ostwald ripening of the early appearing crystals took place over about 5 days. To affect a partial dehydration the reservoir buffer was exchanged in 0.5 M steps to 4 M Na formate/0.1M Na acetate pH 5.2. In separate wells drops of soaking buffer ((1 M Na formate, 5% glycerol, 50 mM Na acetate pH5.2, 10 mM Tris pH 8.3, 150 mM NaCl) was also equilibrated against the 4 M formate/acetate. Crystals were transferred to equilibrated soaking buffer to which 2.5 mM OICR-4425 and 5% DMSO had been added.

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.412	α = 90
b = 71.626	β = 104.782
c = 54.937	γ = 90

Symmetry
Space Group	C 1 2 1

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	APEX II CCD		2011-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54

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	1.71	27.21	96.8	0.026	0.03	0.015	0.999	30.7	3.9		12163			16.44

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	1.71	1.74	80.5		0.127	0.153	0.083	0.989	7.6	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1R28	1.71	27.2	1.36	11936	564	96.77	0.1578	0.156	0.16	0.1936	0.19	23.69

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	18.9246
f_angle_d	1.674
f_chiral_restr	0.0953
f_bond_d	0.0146
f_plane_restr	0.0095

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1024
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	26

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
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.