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Crystal structure of the dimeric form of the bb' domains of human protein disulfide isomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BJ5 PDB entries 3bj5, 3ec3 experimental model PDB 3EC3 PDB entries 3bj5, 3ec3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 295 25% (w/v) polyethylene glycol 1500, 25 mM sodium malonate, 37.5 mM imidazole, 37.5 mM boric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.85 33.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.521 α = 81.85 b = 45.718 β = 92.15 c = 55.149 γ = 80.02
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 210 2007-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 1.7433 CHESS F2
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 2.28 500 92.8 0.068 23.5 7.5 17110 15880 1 1
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) 1 2.28 2.38 92.7 0.403 5.4 7
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 PDB entries 3bj5, 3ec3 2.28 44.55 17110 15714 836 94.6 0.24533 0.24297 0.2434 0.28982 0.2876 RANDOM 41.02
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] 2.03 1.88 0.17 -1.97 -1.05 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.844 r_dihedral_angle_4_deg 16.433 r_dihedral_angle_3_deg 16.328 r_dihedral_angle_1_deg 4.758 r_angle_refined_deg 1.07 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.844 r_dihedral_angle_4_deg 16.433 r_dihedral_angle_3_deg 16.328 r_dihedral_angle_1_deg 4.758 r_angle_refined_deg 1.07 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_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 3034 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling ADSC data collection