1GU4

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.2 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 coefficientSolvent content
3.6966

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.947α = 90
b = 112.326β = 90
c = 74.401γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90IMAGE PLATERIGAKU RAXIS VMIRRORS2001-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XUSPring-8BL45XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.753099.40.09421.73315.4524271631.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.7898.30.4552.0793.96

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1GTW1.829.95390971916990.2320.2320.266RANDOM39.9
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
KeyRefinement Restraint Deviation
c_dihedral_angle_d15
c_scangle_it7.83
c_scbond_it5.65
c_mcangle_it4.71
c_mcbond_it4.11
c_improper_angle_d0.96
c_angle_deg0.8
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d15
c_scangle_it7.83
c_scbond_it5.65
c_mcangle_it4.71
c_mcbond_it4.11
c_improper_angle_d0.96
c_angle_deg0.8
c_bond_d0.004
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 AtomsNumber
Protein Atoms1129
Nucleic Acid Atoms650
Solvent Atoms311
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing