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Structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.9 277 23% PEG550 MME, 50 mM Tris pH 8.9, 1.0 M ammonium formate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 5.110001 75.929558
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.305 α = 90 b = 103.105 β = 91.16 c = 125.826 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 MARMOSAIC 225 mm CCD 2006-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.920 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.7 125 98 0.072 9.9 3.1 18142 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.7 3.9 99.1 0.436 2 3.1
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 (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 2HI7 3.7 125.99 18142 17000 726 97.22 0.33893 0.33733 0.329 0.37903 0.387 RANDOM 160.416
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] -23.32 -2.51 20.62 2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.477 r_dihedral_angle_3_deg 22.549 r_dihedral_angle_4_deg 17.467 r_dihedral_angle_1_deg 8.53 r_angle_refined_deg 1.418 r_angle_other_deg 0.973 r_symmetry_vdw_refined 0.388 r_nbd_refined 0.268 r_nbd_other 0.219 r_xyhbond_nbd_refined 0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.477 r_dihedral_angle_3_deg 22.549 r_dihedral_angle_4_deg 17.467 r_dihedral_angle_1_deg 8.53 r_angle_refined_deg 1.418 r_angle_other_deg 0.973 r_symmetry_vdw_refined 0.388 r_nbd_refined 0.268 r_nbd_other 0.219 r_xyhbond_nbd_refined 0.206 r_nbtor_refined 0.198 r_symmetry_vdw_other 0.136 r_xyhbond_nbd_other 0.111 r_nbtor_other 0.094 r_chiral_restr 0.074 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5112 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement CLARA data collection MOSFLM data reduction SCALA data scaling PHASER phasing