5T1I | pdb_00005t1i

CBX3 chromo shadow domain in complex with histone H3 peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KUP	pdb entry 3kup

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	25% PEG 3350, 0.2 M sodium chloride, 0.1 M Hepes, 5% Ethylene Glycol

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.737	α = 90
b = 34.971	β = 93.32
c = 45.833	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	CCD	ADSC QUANTUM 315r		2013-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9791829	APS	19-ID

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	1.6	45.76	95.5	0.052	0.062	0.033	0.999	14.5	3.4		16432

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	1.6	1.63	65.8		0.86	1.103	0.678	0.524	1	2.3	549

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	pdb entry 3kup	1.6	27.79	15332	1088	95.4	0.197	0.194	0.2057	0.2392	0.2467	thin shells (sftools)	24.65

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]
0.32		0.11	0.83		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.437
r_dihedral_angle_3_deg	12.531
r_dihedral_angle_1_deg	6.049
r_dihedral_angle_4_deg	5.748
r_angle_refined_deg	1.758
r_mcangle_it	1.258
r_angle_other_deg	0.962
r_mcbond_it	0.782
r_mcbond_other	0.782
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1154
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	12

Software

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