5LTY | pdb_00005lty

Homeobox transcription factor CDX2 bound to methylated DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EEA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	PEG 5000, potassium chloride, magnesium chloride, PEG 400,Tris buffer

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.882	α = 90
b = 46.613	β = 98.46
c = 120.428	γ = 90

Symmetry
Space Group	I 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	ADSC QUANTUM 315r		2016-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9724	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.66	63.29	98.5	0.043	0.999	15	3.3		10979			73.25

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.66	2.79	96.7		0.637	0.647	1.7	3.1

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	5EEA	2.66	63.29	10459	519	98.45	0.2039	0.202	0.2048	0.2422	0.2389	RANDOM	77.843

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]
1.73		0.76	-4.67		2.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.011
r_dihedral_angle_3_deg	21.368
r_dihedral_angle_1_deg	20.305
r_dihedral_angle_4_deg	15.037
r_mcangle_it	3.229
r_angle_refined_deg	2.161
r_mcbond_it	1.988
r_mcbond_other	1.98
r_angle_other_deg	1.69
r_chiral_restr	0.176
r_bond_refined_d	0.017
r_gen_planes_refined	0.014
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1243
Nucleic Acid Atoms	1480
Solvent Atoms	34
Heterogen Atoms

Software

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