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Crystal structure of transcription factor NtcA from Synechococcus elongatus bound to 2-oxoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XGX PDB ENTRY 2XGX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 NTCA PROTEIN WAS AT 4.7 MG/ML 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, 10 MM 2-OXOGLUTARATE (2OG). CRYSTALLIZATION SOLUTION: 0.1 M BIS-TRIS PH 5.5, 11 % PEG 10000, 0.15 M AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 3.35 63.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.22 α = 90 b = 70.81 β = 90 c = 149.96 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 CCD 2009-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.3 75 99.8 0.05 13.3 7.1 32971 1.8 47.6
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 2.3 2.42 100 0.44 1.8 7.3
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2XGX 2.3 50 31296 1673 99.77 0.20566 0.20393 0.2271 0.23769 0.2506 RANDOM 47.081
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] 0.48 1.04 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.823 r_dihedral_angle_4_deg 21.042 r_dihedral_angle_3_deg 19.307 r_dihedral_angle_1_deg 6.542 r_scangle_it 3.234 r_scbond_it 2.019 r_angle_refined_deg 1.563 r_mcangle_it 1.251 r_angle_other_deg 0.953 r_mcbond_it 0.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.823 r_dihedral_angle_4_deg 21.042 r_dihedral_angle_3_deg 19.307 r_dihedral_angle_1_deg 6.542 r_scangle_it 3.234 r_scbond_it 2.019 r_angle_refined_deg 1.563 r_mcangle_it 1.251 r_angle_other_deg 0.953 r_mcbond_it 0.684 r_mcbond_other 0.157 r_chiral_restr 0.096 r_bond_refined_d 0.015 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_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 3396 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing