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structure of xylose-binding transcription activator xylR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 1.3 M Li2SO4
100 mM Tris pH=8.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.81 56.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.071 α = 90 b = 70.071 β = 90 c = 215.403 γ = 90
Symmetry Space Group P 41 21 2
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 2009-08-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 0.95689 ALS 8.3.1
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 2.9 107.83 100 0.079 29.2 8.6 12704 12704 3 2 70.333
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 2.9 3.06 100 0.385 7.6 8.7 1789
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 (All) 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 2.9 66.67 12022 12022 615 100 0.22204 0.22204 0.2193 0.2219 0.27916 0.2821 RANDOM 55.101
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] 0.07 0.07 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.733 r_dihedral_angle_3_deg 19.359 r_dihedral_angle_4_deg 12.216 r_dihedral_angle_1_deg 5.857 r_scangle_it 1.909 r_angle_refined_deg 1.275 r_scbond_it 1.15 r_mcangle_it 0.816 r_mcbond_it 0.487 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.733 r_dihedral_angle_3_deg 19.359 r_dihedral_angle_4_deg 12.216 r_dihedral_angle_1_deg 5.857 r_scangle_it 1.909 r_angle_refined_deg 1.275 r_scbond_it 1.15 r_mcangle_it 0.816 r_mcbond_it 0.487 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.241 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.088 r_bond_refined_d 0.01 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_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 3067 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 10
Software Software Software Name Purpose Blu-Ice data collection SOLVE phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling