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crystal structure of C/EBPbeta bZip homodimer bound to a DNA fragment from the tom-1A promoter
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 0.2211 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
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