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Crystal Structure of Yeast Protein Disulfide Isomerase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 sodium cacodylate, magnesium chloride, PEG 2000 MME, barium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.87 57.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.56 α = 90 b = 136.56 β = 90 c = 69.524 γ = 90
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 315 2005-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 24847
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 20 23557 1246 98.7 0.193 0.191 0.246 0.2818 RANDOM 66.965
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] -1.75 -1.75 3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.729 r_dihedral_angle_4_deg 19.371 r_dihedral_angle_3_deg 18.08 r_dihedral_angle_1_deg 8.219 r_scangle_it 2.7 r_scbond_it 1.758 r_angle_refined_deg 1.624 r_mcangle_it 1.093 r_angle_other_deg 0.883 r_mcbond_it 0.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.729 r_dihedral_angle_4_deg 19.371 r_dihedral_angle_3_deg 18.08 r_dihedral_angle_1_deg 8.219 r_scangle_it 2.7 r_scbond_it 1.758 r_angle_refined_deg 1.624 r_mcangle_it 1.093 r_angle_other_deg 0.883 r_mcbond_it 0.854 r_xyhbond_nbd_other 0.29 r_symmetry_hbond_refined 0.264 r_symmetry_vdw_other 0.234 r_xyhbond_nbd_refined 0.231 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.223 r_nbd_other 0.186 r_nbtor_refined 0.186 r_mcbond_other 0.145 r_chiral_restr 0.097 r_nbtor_other 0.091 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3820 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing