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Crystal structure of C/EBPBETA BZIP homodimer bound to a high affinity DNA fragment
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 0.2236 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
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