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Structure of the self-association domain of the chromatin looping factor LDB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 18.6% PEG3350, 140 mM sodium phosphate dibasic 2 VAPOR DIFFUSION, SITTING DROP 293 18.6% PEG3350, 140 mM sodium phosphate dibasic, crystal soaked overnight in mother liquor containing 10 mM ethylmercury thiosalicylic acid
Crystal Properties Matthews coefficient Solvent content 2.86 56.99 2.86 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.869 α = 90 b = 81.869 β = 90 c = 66.828 γ = 120
Symmetry Space Group P 32 2 1
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 2014-09-27 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC QUANTUM 210r 2015-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2 2 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.5 35.5 99.7 0.083 0.087 0.027 0.998 14.7 10.7 9212 75.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 100 1.213 1.271 0.381 0.929 2.5 11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 35.48 8696 496 99.47 0.2463 0.2448 0.2488 0.2708 0.2647 RANDOM 87.291
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] 2.28 1.14 2.28 -7.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.685 r_dihedral_angle_4_deg 18.234 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 5.46 r_angle_refined_deg 1.14 r_angle_other_deg 1.013 r_chiral_restr 0.032 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.685 r_dihedral_angle_4_deg 18.234 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 5.46 r_angle_refined_deg 1.14 r_angle_other_deg 1.013 r_chiral_restr 0.032 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1213 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing