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Crystal structure of C/EBPBETA BZIP homodimer bound to a DNA fragment from the MIM-1 promoter
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 6.5 0.08 M MAGNESIUM ACETATE, 15.0% V/V PEG 400, 0.05 M SODIUM CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX CONCENTRATION WAS 12 MG/ML WITH ADDITION OF 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 3.74 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.596 α = 90 b = 113.037 β = 90 c = 74.498 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 2.08 30 99.4 0.069 24.364 6.088 25871 44
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 2.08 2.12 97.3 0.468 3.13 4.55
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 2.1 29.74 25194 1228 99.2 0.229 0.229 0.2179 0.277 RANDOM 48.3
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] 4.88 -3.32 -1.57
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 14.7 c_scangle_it 9.73 c_scbond_it 7.35 c_mcangle_it 6.25 c_mcbond_it 5.23 c_improper_angle_d 1.05 c_angle_deg 0.9 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 14.7 c_scangle_it 9.73 c_scbond_it 7.35 c_mcangle_it 6.25 c_mcbond_it 5.23 c_improper_angle_d 1.05 c_angle_deg 0.9 c_bond_d 0.005 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 224 Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing