1GU4 | pdb_00001gu4

Crystal structure of C/EBPBETA BZIP homodimer bound to a high affinity DNA fragment

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		0.2 M POTASSIUM CHLORIDE, 0.01 M MAGNESIUM SULFATE, 10.0% V/V PEG 400, 0.05 M MES BUFFER PH 6.0, PROTEIN-DNA COMPLEX CONCENTRATION WAS 12 MG/ML AND CONTAINS 0.01 M DTT, PROTEIN:DNA RATIO WAS 1:1.2. FOR CRYOPROTECTION THE CONCENTRATION OF PEG 400 WAS ADJUSTED TO 36% V/V

Crystal Properties
Matthews coefficient	Solvent content
3.69	66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.947	α = 90
b = 112.326	β = 90
c = 74.401	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	90	IMAGE PLATE	RIGAKU RAXIS V	MIRRORS	2001-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU		SPring-8	BL45XU

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	1.75	30	99.4	0.094	21.7331	5.452		42716			31.9

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	1.75	1.78	98.3		0.455	2.079	3.96

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 1GTW	1.8	29.95	39097	1916	99	0.232	0.232	0.22	0.266	RANDOM	39.9

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]
6.9			-3.12		-3.78

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	15
c_scangle_it	7.83
c_scbond_it	5.65
c_mcangle_it	4.71
c_mcbond_it	4.11
c_improper_angle_d	0.96
c_angle_deg	0.8
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	311
Heterogen Atoms

Software

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