6V2H | pdb_00006v2h

Crystal structure of CDYL2 in complex with H3tK27me3

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6V41	an early version of PDB entry 6V41 (CDY1 in complex with a histone peptide)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	23% PEG3350, 0.25 M ammonium dihydrogen phosphate, 0.1 M sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
5.49	77.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.75	α = 90
b = 210.75	β = 90
c = 67.2	γ = 120

Symmetry
Space Group	H 3

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	MARMOSAIC 300 mm CCD		2015-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97957	CLSI	08ID-1

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	2.6	63.06	100	0.099	0.109	0.045	0.997	14.8	5.9		34195

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	2.6	2.67	100		0.997	1.095	0.452	0.658		5.9

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	an early version of PDB entry 6V41 (CDY1 in complex with a histone peptide)	2.6	63.14	31961	2234	99.97	0.2185	0.2173	0.22	0.2366	0.24	58.187

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]
-0.6	-0.3		-0.6		1.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.67
r_dihedral_angle_3_deg	14.703
r_dihedral_angle_4_deg	12.522
r_dihedral_angle_1_deg	5.394
r_angle_refined_deg	1.362
r_angle_other_deg	0.911
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.67
r_dihedral_angle_3_deg	14.703
r_dihedral_angle_4_deg	12.522
r_dihedral_angle_1_deg	5.394
r_angle_refined_deg	1.362
r_angle_other_deg	0.911
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3322
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
xia2	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.