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Crystal structure of the BTB domain from the Miz-1/ZBTB17 transcription regulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R29 Single chain poly-alanine model of PDB code 1R29 residues 7-128, except where residues were identical between Miz1 and 1R29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 75 mM zinc acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.47 50.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.023 α = 90 b = 80.935 β = 90 c = 95.713 γ = 90
Symmetry Space Group P 21 21 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 315r mirrors 2006-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
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 2.59 90 98.5 0.0952 10.87 3.67 8404 -3
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) 2.59 2.7 48.9 0.4483 3.55 0.96 92
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Single chain poly-alanine model of PDB code 1R29 residues 7-128, except where residues were identical between Miz1 and 1R29 2.59 41.2 7990 383 98.82 0.22688 0.22493 0.2248 0.2665 0.2697 RANDOM 29.383
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.807 r_dihedral_angle_3_deg 17.466 r_dihedral_angle_4_deg 9.74 r_dihedral_angle_1_deg 4.872 r_scangle_it 1.644 r_scbond_it 1.258 r_angle_refined_deg 1.145 r_mcangle_it 0.8 r_mcbond_it 0.431 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.807 r_dihedral_angle_3_deg 17.466 r_dihedral_angle_4_deg 9.74 r_dihedral_angle_1_deg 4.872 r_scangle_it 1.644 r_scbond_it 1.258 r_angle_refined_deg 1.145 r_mcangle_it 0.8 r_mcbond_it 0.431 r_nbtor_refined 0.294 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.15 r_symmetry_metal_ion_refined 0.08 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1784 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 14
Software Software Software Name Purpose ADSC data collection EPMR phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling