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Crystal structure of transcription factor NtcA from Synechococcus elongatus in complex with its transcriptional co- activator PipX and its target DNA (Crystal I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.15 PipX-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: 0,2M MgSO4 and 20% PEG3350. Cryo protectant: 39% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.26 α = 90 b = 68.18 β = 115.07 c = 126.25 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 2M 2012-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9173 Diamond I04-1
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 3.8 114.4 92.2 0.193 3 2.8 16087
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 3.8 4.01 0.398
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 3.8 64.14 15269 811 91.62 0.31739 0.3154 0.3085 0.35385 0.35 RANDOM 69.248
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] -2.83 1.75 1.38 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.204 r_dihedral_angle_2_deg 10.407 r_long_range_B_refined 7.665 r_long_range_B_other 7.665 r_dihedral_angle_1_deg 4.477 r_mcangle_it 4.01 r_mcangle_other 4.01 r_scangle_other 3.316 r_mcbond_it 2.426 r_mcbond_other 2.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.204 r_dihedral_angle_2_deg 10.407 r_long_range_B_refined 7.665 r_long_range_B_other 7.665 r_dihedral_angle_1_deg 4.477 r_mcangle_it 4.01 r_mcangle_other 4.01 r_scangle_other 3.316 r_mcbond_it 2.426 r_mcbond_other 2.426 r_scbond_it 1.934 r_scbond_other 1.933 r_angle_refined_deg 1.758 r_angle_other_deg 0.668 r_chiral_restr 0.115 r_bond_other_d 0.019 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 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 9543 Nucleic Acid Atoms 2460 Solvent Atoms Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOSFLM data reduction PHASER phasing