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Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B72 PDB ENTRY 1B72
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 292 PEG 4000, hepes, cobaltic hexamine, dithiothrietol, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 3.03 59.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.769 α = 90 b = 114.853 β = 90 c = 108.17 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 100 CCD ADSC QUANTUM 4 2000-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 20 95.6 0.065 22.3 4.3 28839 31.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 20 94.1 0.26 4.9 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1B72 1.9 19.97 30169 28839 2873 95.6 0.233 0.233 0.2407 0.268 0.2752 RANDOM IN CNS 48.7
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] -2.44 -8.53 10.98
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.5 c_scangle_it 2.98 c_mcangle_it 2.48 c_scbond_it 1.97 c_mcbond_it 1.54 c_angle_deg 1.43 c_improper_angle_d 1.37 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.5 c_scangle_it 2.98 c_mcangle_it 2.48 c_scbond_it 1.97 c_mcbond_it 1.54 c_angle_deg 1.43 c_improper_angle_d 1.37 c_bond_d 0.01 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 1268 Nucleic Acid Atoms 814 Solvent Atoms 247 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement