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Crystal structure of the superoxide reductase from Treponema pallidum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 3350, magnesium chloride, trisHCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.2 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.311 α = 90 b = 59.946 β = 104.96 c = 65.52 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 4 mirrors 2004-07-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.739, 1.033 ESRF BM14
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 1.55 63.25 82.4 0.046 0.043 8.8 6.9 53624 53059 2 2 19.3
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) 1.55 1.63 82.4 0.196 0.177 4.3 5.4 3751
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 MAD THROUGHOUT 1.55 63.25 2 2 53277 50599 2678 82.13 0.189 0.1845 0.18183 0.234 0.23522 0.2822 RANDOM 14.824
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] -1.39 0.26 1.66 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.328 r_sphericity_free 6.112 r_scangle_it 4.747 r_scbond_it 3.122 r_sphericity_bonded 2.47 r_mcangle_it 2.268 r_rigid_bond_restr 1.81 r_angle_refined_deg 1.765 r_mcbond_it 1.545 r_angle_other_deg 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.328 r_sphericity_free 6.112 r_scangle_it 4.747 r_scbond_it 3.122 r_sphericity_bonded 2.47 r_mcangle_it 2.268 r_rigid_bond_restr 1.81 r_angle_refined_deg 1.765 r_mcbond_it 1.545 r_angle_other_deg 0.886 r_symmetry_vdw_other 0.357 r_symmetry_vdw_refined 0.334 r_nbd_other 0.261 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.107 r_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_other 0.02 r_gen_planes_refined 0.013 r_metal_ion_refined 0.012 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3724 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction CCP4 data scaling PHENIX phasing