☰ Navigation Tabs
Crystal structure of the oxidized T176V DsbA1 mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DVW PDB entry 3DVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 293 Citrate, pH 9.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.96 37.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.307 α = 90 b = 47.615 β = 90 c = 79.82 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 315r 2008-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.97973 ESRF BM30A
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 1.45 44 99.4 0.061 0.058 6.2 6.4 30676 14.2
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) 1.45 1.52 96.4 0.264 0.233 3 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3DVW 1.45 40 27530 3085 99.75 0.19452 0.19093 0.1891 0.22625 0.2249 RANDOM 16.256
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] -0.31 0.49 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.52 r_dihedral_angle_4_deg 13.168 r_dihedral_angle_3_deg 12.532 r_dihedral_angle_1_deg 5.073 r_sphericity_free 3.422 r_scangle_it 2.912 r_sphericity_bonded 2.351 r_scbond_it 2.129 r_rigid_bond_restr 1.507 r_mcangle_it 1.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.52 r_dihedral_angle_4_deg 13.168 r_dihedral_angle_3_deg 12.532 r_dihedral_angle_1_deg 5.073 r_sphericity_free 3.422 r_scangle_it 2.912 r_sphericity_bonded 2.351 r_scbond_it 2.129 r_rigid_bond_restr 1.507 r_mcangle_it 1.402 r_angle_refined_deg 1.171 r_mcbond_it 0.906 r_nbtor_refined 0.307 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.182 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1541 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing