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Crystal Structure of the second catalytic domain of protein disulfide isomerase P5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EF0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 294 0.1M citric acid, 25% PEG3350, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.89 34.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.731 α = 93.43 b = 40.637 β = 112.66 c = 41.488 γ = 101.22
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 2012-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9760 CHESS A1
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 1.8 50 96.76 0.061 15.8 2.4 17641 17069 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 1.8 1.83 86.01 0.268 2.5 1.9 1136
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 4EF0 1.81 39.41 1 17641 17069 931 96.76 0.17745 0.17515 0.1754 0.219 0.2219 RANDOM 24.858
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 -0.25 -0.73 0.3 -0.21 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.232 r_dihedral_angle_3_deg 16.059 r_dihedral_angle_4_deg 14.653 r_dihedral_angle_1_deg 5.818 r_scangle_it 4.756 r_scbond_it 2.876 r_mcangle_it 2.005 r_angle_refined_deg 1.363 r_mcbond_it 1.226 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.232 r_dihedral_angle_3_deg 16.059 r_dihedral_angle_4_deg 14.653 r_dihedral_angle_1_deg 5.818 r_scangle_it 4.756 r_scbond_it 2.876 r_mcangle_it 2.005 r_angle_refined_deg 1.363 r_mcbond_it 1.226 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.095 r_symmetry_hbond_refined 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1732 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling