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Crystal structure of E.coli 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, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.66 53.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.683 α = 90 b = 59.668 β = 90 c = 65.207 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 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 44.023 97.4 0.122 0.122 4.8 2.8 19836 19836 11.2
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 99.3 0.451 0.451 1.6 2.7 2915
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.74 44.02 19815 19815 1027 96.63 0.171 0.171 0.169 0.1688 0.204 0.2046 RANDOM 13.706
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.541 r_dihedral_angle_4_deg 17.239 r_dihedral_angle_3_deg 16.579 r_dihedral_angle_1_deg 5.398 r_scangle_it 3.047 r_scbond_it 1.93 r_angle_refined_deg 1.504 r_mcangle_it 1.226 r_mcbond_it 0.732 r_nbd_refined 0.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.541 r_dihedral_angle_4_deg 17.239 r_dihedral_angle_3_deg 16.579 r_dihedral_angle_1_deg 5.398 r_scangle_it 3.047 r_scbond_it 1.93 r_angle_refined_deg 1.504 r_mcangle_it 1.226 r_mcbond_it 0.732 r_nbd_refined 0.345 r_nbtor_refined 0.29 r_symmetry_hbond_refined 0.229 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1099 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 215
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction SHELXS phasing