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Crystal structure of chemically-reduced E.coli nrfB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OZY OXIDISED STRUCTURE OF NRFB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 289 Purified NrfB was concentrated to 8 mg/ml before crystallization. Crystals were obtained by the vapour diffusion method under anaerobic conditions using 250 mM tri-sodium citrate, 10 mM Na2S2O4 and 20 % (v/v) isopropanol in 100 mM sodium HEPES pH 7.5. Crystals were soaked in 100 mM Na2S2O4 prior to harvesting, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.65 53.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.727 α = 90 b = 59.433 β = 90 c = 65.318 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 CCD ADSC QUANTUM 315 2006-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.74 43.98 94 0.131 0.131 4.7 4.2 19070 8.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.83 97 0.433 0.433 1.5 4 2846
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 OXIDISED STRUCTURE OF NRFB 1.74 7.99 18843 18843 957 93.16 0.161 0.161 0.159 0.1588 0.192 0.1915 RANDOM 10.925
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.1 r_dihedral_angle_4_deg 22.656 r_dihedral_angle_3_deg 12.667 r_dihedral_angle_1_deg 5.523 r_scangle_it 2.88 r_scbond_it 1.88 r_angle_refined_deg 1.577 r_mcangle_it 1.25 r_mcbond_it 0.772 r_nbd_refined 0.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.1 r_dihedral_angle_4_deg 22.656 r_dihedral_angle_3_deg 12.667 r_dihedral_angle_1_deg 5.523 r_scangle_it 2.88 r_scbond_it 1.88 r_angle_refined_deg 1.577 r_mcangle_it 1.25 r_mcbond_it 0.772 r_nbd_refined 0.355 r_nbtor_refined 0.295 r_symmetry_vdw_refined 0.18 r_symmetry_hbond_refined 0.127 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.099 r_metal_ion_refined 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1099 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 215
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction MOLREP phasing