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Crystal structure of yeast protein disulfide isomerase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B5E PDB ENTRY 2B5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 100mM NaCacodylate 6.5, 0.35M MgCl2, 29% PEG2000 MME, 1mM BaCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.921 α = 90 b = 123.154 β = 90 c = 75.721 γ = 90
Symmetry Space Group C 2 2 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 4 2004-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C
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 3.7 50 99.8 0.092 18.3 5.6 6049
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 3.7 3.76 99.7 0.696 2.1 5.5
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2B5E 3.7 19.81 5738 306 99.95 0.2442 0.23919 0.2464 0.33984 0.2393 RANDOM 168.842
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] -0.32 -0.29 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.079 r_dihedral_angle_3_deg 20.373 r_dihedral_angle_4_deg 19.954 r_dihedral_angle_1_deg 8.147 r_angle_refined_deg 1.18 r_angle_other_deg 0.798 r_scangle_it 0.515 r_scbond_it 0.325 r_mcangle_it 0.296 r_mcbond_it 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.079 r_dihedral_angle_3_deg 20.373 r_dihedral_angle_4_deg 19.954 r_dihedral_angle_1_deg 8.147 r_angle_refined_deg 1.18 r_angle_other_deg 0.798 r_scangle_it 0.515 r_scbond_it 0.325 r_mcangle_it 0.296 r_mcbond_it 0.25 r_nbd_refined 0.223 r_nbtor_refined 0.185 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.181 r_nbd_other 0.172 r_symmetry_vdw_other 0.172 r_symmetry_hbond_refined 0.163 r_nbtor_other 0.084 r_chiral_restr 0.069 r_xyhbond_nbd_other 0.028 r_mcbond_other 0.024 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3864 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CBASS data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing