7CNA

Crystal structure of Spindlin1/C11orf84 complex bound to histone H3K4me3K9me3 peptide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.1 M sodium cacodylate pH 6.5, 35% PEG3350, 5% glycerol, 2% Benzamidine hydrochloride

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.603	α = 90
b = 101.184	β = 91.41
c = 56.615	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS EIGER X 16M		2018-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.979	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.6	35.11	98.6	0.026	32.7	3.2		66759

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66			0.11

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4MZF	1.6	35.11	64741	2002	98.59	0.1727	0.1718	0.2007	RANDOM	20.031

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
r_dihedral_angle_2_deg	34.058
r_dihedral_angle_3_deg	13.419
r_dihedral_angle_4_deg	12.513
r_dihedral_angle_1_deg	7.512
r_angle_refined_deg	1.798
r_angle_other_deg	1.468
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.058
r_dihedral_angle_3_deg	13.419
r_dihedral_angle_4_deg	12.513
r_dihedral_angle_1_deg	7.512
r_angle_refined_deg	1.798
r_angle_other_deg	1.468
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3891
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

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 R01GM133198.