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NtcA from Synechococcus elongatus: active and inactive
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 8.3 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. CRYSTALLIZATION SOLUTION: 0.2 M POTASSIUM CITRATE PH 8.3, 20 % PEG-3350.
Crystal Properties Matthews coefficient Solvent content 2.38 48.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.391 α = 90 b = 110.391 β = 90 c = 219.6 γ = 120
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 3.05 87.7 100 0.12 5.6 11.2 28882 1.8 69.1
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 3.05 3.21 100 0.43 1.8 11.4
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 3.05 50 27354 1461 99.98 0.20828 0.20621 0.2474 0.2576 RANDOM 54.478
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] 0.78 0.39 0.78 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_3_deg 21.719 r_dihedral_angle_4_deg 19.487 r_dihedral_angle_1_deg 6.295 r_scangle_it 1.937 r_angle_refined_deg 1.222 r_scbond_it 1.033 r_angle_other_deg 0.892 r_mcangle_it 0.746 r_mcbond_it 0.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_3_deg 21.719 r_dihedral_angle_4_deg 19.487 r_dihedral_angle_1_deg 6.295 r_scangle_it 1.937 r_angle_refined_deg 1.222 r_scbond_it 1.033 r_angle_other_deg 0.892 r_mcangle_it 0.746 r_mcbond_it 0.385 r_chiral_restr 0.078 r_mcbond_other 0.047 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 9506 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing