1GTW | pdb_00001gtw

crystal structure of C/EBPbeta bZip homodimer bound to a DNA fragment from the tom-1A promoter

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H8A	PDB ENTRY 1H8A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.2 M POTASSIUM CHLORIDE, 0.1 M MAGNESIUM ACETATE, 10.0% W/V PEG 8000, 0.05 M SODIUM CACODYLATE CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX SOLUTION CONTAINS 0.01 M DTT AND 0.005 M NAN3, PROTEIN:DNA RATIO IS 1:1.2

Crystal Properties
Matthews coefficient	Solvent content
3.7	66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.938	α = 90
b = 112.533	β = 90
c = 74.349	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	RIGAKU IMAGE PLATE RAXIS IV		1998-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2		SPring-8	BL44B2

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	1.7	20	95.8	0.052	21.0506	4.008		44759			34.2

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	1.7	1.76	82.9		0.43	1.343	2.43

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1H8A	1.85	19.87	35717	1809	98	0.231	0.231	0.22	0.271	RANDOM	42.9

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]
7.95			-5.16		-2.79

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	15.7
c_scangle_it	9.23
c_scbond_it	6.94
c_mcangle_it	5.68
c_mcbond_it	4.97
c_improper_angle_d	1.13
c_angle_deg	1
c_bond_d	0.004
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1129
Nucleic Acid Atoms	650
Solvent Atoms	316
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing