☰ Navigation Tabs
Crystal structure of the b'-a' domain of thermophilic fungal protein disulfide isomerase (oxidized form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2KP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% PEG4000, 100mM Tris-HCl pH 8.5, 200mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.31 α = 90 b = 96.31 β = 90 c = 69.49 γ = 120
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 RAYONIX MX-225 2011-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.3 50 99.9 0.088 32 5.8 10825 10809 -3 30.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.36 100 0.368 6.9 5.9 490
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2KP1 3.3 20 10809 10256 520 99.67 0.226 0.221 0.313 0.3029 RANDOM 85.399
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] 0.45 0.45 0.45 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.049 r_dihedral_angle_4_deg 32.146 r_dihedral_angle_3_deg 18.918 r_dihedral_angle_1_deg 6.392 r_angle_refined_deg 1.508 r_angle_other_deg 0.92 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.049 r_dihedral_angle_4_deg 32.146 r_dihedral_angle_3_deg 18.918 r_dihedral_angle_1_deg 6.392 r_angle_refined_deg 1.508 r_angle_other_deg 0.92 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5637 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling