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DNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (Crystal form I)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 293 6% PEG4000, 200mM KCl, 100mM MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.35 63.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.75 α = 90 b = 70.75 β = 90 c = 601.56 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 225 mm CCD 2009-08-03 M SINGLE WAVELENGTH 2 1 x-ray CCD MARMOSAIC 225 mm CCD 2009-08-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA 2 SYNCHROTRON SLS BEAMLINE X06DA 1.2551, 1.2556, 1.2425 SLS X06DA
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 3 30 98.9 0.182 11.8 13.1 19386 19172 2 41.7
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) 1,2 3 3.1 89.9 0.591 2.6 9.9 1744
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 3.01 29.71 19172 18211 959 100 0.22387 0.221 0.2204 0.27778 0.2706 RANDOM 60.109
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] 1.35 0.68 1.35 -2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.319 r_dihedral_angle_4_deg 19.337 r_dihedral_angle_3_deg 19.009 r_dihedral_angle_1_deg 6.526 r_scangle_it 1.633 r_angle_refined_deg 1.341 r_scbond_it 0.979 r_mcangle_it 0.711 r_mcbond_it 0.368 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.319 r_dihedral_angle_4_deg 19.337 r_dihedral_angle_3_deg 19.009 r_dihedral_angle_1_deg 6.526 r_scangle_it 1.633 r_angle_refined_deg 1.341 r_scbond_it 0.979 r_mcangle_it 0.711 r_mcbond_it 0.368 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 3411 Nucleic Acid Atoms 896 Solvent Atoms 33 Heterogen Atoms 2
Software Software Software Name Purpose SHARP phasing REFMAC refinement XDS data reduction XSCALE data scaling