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Crystal structure of transcription factor NtcA from Synechococcus elongatus in complex with its target DNA.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.15 NTCA-DNA complex was in 50 mM sodium citrate pH 6.5, 0.5 M NaCl, 5 mM magnesium cloride, 50 mM arginine hydrocloride, 50 mM Na L-glutamate and 10mM 2-oxoglutarate. CRYSTALLIZATION SOLUTION: 0,1M Bis-Tris, pH 6,5, 28% PEG monomethyl ether 2K. Cryo protectant: 38% PEG monomethyl ether
Crystal Properties Matthews coefficient Solvent content 2.83 56.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.854 α = 90 b = 46.935 β = 98.62 c = 139.737 γ = 90
Symmetry Space Group C 1 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 210r 2010-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.9797 ESRF BM16
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 3 24.2 98.5 0.085 7.9 2.7 15466
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 3 3.16 0.429
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 3 24.17 14688 767 97.54 0.21585 0.2138 0.2254 0.2525 0.2558 RANDOM 67.789
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] -3.64 0.91 -4.99 7.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.667 r_long_range_B_refined 10.241 r_long_range_B_other 10.241 r_dihedral_angle_2_deg 7.704 r_dihedral_angle_1_deg 6.588 r_scangle_other 4.911 r_mcangle_other 4.389 r_mcangle_it 4.388 r_scbond_it 3.026 r_scbond_other 3.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.667 r_long_range_B_refined 10.241 r_long_range_B_other 10.241 r_dihedral_angle_2_deg 7.704 r_dihedral_angle_1_deg 6.588 r_scangle_other 4.911 r_mcangle_other 4.389 r_mcangle_it 4.388 r_scbond_it 3.026 r_scbond_other 3.025 r_mcbond_it 2.67 r_mcbond_other 2.67 r_angle_refined_deg 1.668 r_angle_other_deg 0.425 r_chiral_restr 0.098 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3305 Nucleic Acid Atoms 1230 Solvent Atoms 4 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction MOLREP phasing