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Near atomic resolution crystal structure of Sco5413, a MarR family transcriptional regulator from Streptomyces coelicolor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 HANGING DROP VAPOUR DIFFUSION AT 291 K. DROPS CONSISTED OF 1 MICROLITRE OF PROTEIN AT 10 MG/ML IN 50 MM HEPES PH 7.5, 500 MM NACL PLUS 1 MICROLITRE OF PRECIPITANT SOLUTION COMPRISED OF 0.2 M POTASSIUM NITRATE, 25% PEG 3350, 6% MPD, 15% GLYCEROL, 1 MM SPERMIDINE
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.4 α = 90 b = 65.65 β = 90 c = 69.72 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 315 2011-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.25 69.72 100 0.09 11.5 8.3 81107 14.6
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 1.25 1.28 100 0.71 2.6 6
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 SIRAS THROUGHOUT NONE 1.25 47.8 76966 4062 99.94 0.14861 0.14718 0.1568 0.17509 0.1804 RANDOM 15.9
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] 0.32 0.29 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.662 r_sphericity_free 22.134 r_dihedral_angle_4_deg 19.882 r_dihedral_angle_3_deg 12.269 r_sphericity_bonded 8.459 r_dihedral_angle_1_deg 4.572 r_rigid_bond_restr 2.383 r_angle_refined_deg 1.409 r_angle_other_deg 0.947 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.662 r_sphericity_free 22.134 r_dihedral_angle_4_deg 19.882 r_dihedral_angle_3_deg 12.269 r_sphericity_bonded 8.459 r_dihedral_angle_1_deg 4.572 r_rigid_bond_restr 2.383 r_angle_refined_deg 1.409 r_angle_other_deg 0.947 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2089 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHENIX phasing