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The SoxAX Complex of Rhodovulum Sulfidophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H33 PDB ENTRY 1H33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 15% (w/v) PEG 4K, 0.2 M magnesium acetate, 100 mM sodium MES buffer pH 6.5. The crystals could be cryoprotected by transferring them to stabilization solution containing 25% (v/v) ethylene glycol. , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.59 52.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.975 α = 90 b = 102.949 β = 110.22 c = 115.706 γ = 90
Symmetry Space Group P 1 21 1
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 MAR CCD 165 mm 2005-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 2.345 108.577 96 0.086 0.086 7.4 2.7 71803 71803 26.4
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) 2.34 2.47 81.5 0.189 0.189 3.7 1.5 8867
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 PDB ENTRY 1H33 2.35 50 71773 71773 3633 96.03 0.189 0.189 0.187 0.1869 0.242 0.2407 RANDOM 14.774
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] 0.43 0.44 -0.18 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.341 r_dihedral_angle_3_deg 15.596 r_dihedral_angle_4_deg 15.349 r_dihedral_angle_1_deg 5.847 r_scangle_it 2.078 r_angle_refined_deg 1.331 r_scbond_it 1.305 r_mcangle_it 0.814 r_mcbond_it 0.541 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.341 r_dihedral_angle_3_deg 15.596 r_dihedral_angle_4_deg 15.349 r_dihedral_angle_1_deg 5.847 r_scangle_it 2.078 r_angle_refined_deg 1.331 r_scbond_it 1.305 r_mcangle_it 0.814 r_mcbond_it 0.541 r_nbtor_refined 0.298 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.15 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12213 Nucleic Acid Atoms Solvent Atoms 939 Heterogen Atoms 516
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection MOSFLM data reduction MOLREP phasing