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Crystal structure of the complex of NtcA with its transcriptional co- activator PipX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XHK PDB ENTRY 2XHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 NTCA-PIPX COMPLEX WAS IN 50 MM SODIUM CITRATE PH 6.5, 0.5 M NACL, 5 MM MAGNESIUM CHLORIDE, 50 MM ARGININE HYDROCHLORIDE, 50 MM NA L-GLUTAMATE, AND 10 MM 2-OXOGLUTARATE. CRYSTALLIZATION SOLUTION: 50 MM MES PH 5.5, 1M SODIUM MALONATE 10 MM MANGANESE CHLORIDE, 2% MPD, 5% DMSO.
Crystal Properties Matthews coefficient Solvent content 2 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.02 α = 90 b = 52.02 β = 90 c = 227.73 γ = 90
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 2009-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 ESRF BM16
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 2.25 56.89 98.9 0.08 7.1 6.9 28245 2 36.2
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 2.25 2.37 98.9 0.4 2 5.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2XHK 2.25 25 26813 1420 98.98 0.2157 0.21413 0.24533 0.2882 RANDOM 35.677
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] -0.17 -0.17 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.474 r_dihedral_angle_4_deg 20.187 r_dihedral_angle_3_deg 16.911 r_dihedral_angle_1_deg 6.793 r_scangle_it 2.999 r_scbond_it 1.813 r_angle_refined_deg 1.419 r_mcangle_it 1.171 r_angle_other_deg 0.896 r_mcbond_it 0.617
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.474 r_dihedral_angle_4_deg 20.187 r_dihedral_angle_3_deg 16.911 r_dihedral_angle_1_deg 6.793 r_scangle_it 2.999 r_scbond_it 1.813 r_angle_refined_deg 1.419 r_mcangle_it 1.171 r_angle_other_deg 0.896 r_mcbond_it 0.617 r_mcbond_other 0.132 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4744 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing