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Crystal structure of the b'-a' domain of thermophilic fungal protein disulfide isomerase (reduced 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 4.6 293 36% PEG2000MME, 100mM sodium acetate pH 4.6, 200mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.77 α = 105.92 b = 67.75 β = 113.13 c = 70.25 γ = 96.59
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 2012-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00000 NSRRC BL13B1
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 1.85 50 92.3 0.055 26.2 2.1 88599 81751 -3 68.4
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 1.85 1.88 81.7 0.378 1.5 2 3648
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 1.85 20 81751 77551 4085 92.09 0.24 0.238 0.278 0.2869 RANDOM 41.453
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] 0.07 -3.18 -1.43 4.08 0.26 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.657 r_dihedral_angle_4_deg 23.005 r_dihedral_angle_3_deg 17.795 r_dihedral_angle_1_deg 6.105 r_angle_refined_deg 1.672 r_angle_other_deg 1.361 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.657 r_dihedral_angle_4_deg 23.005 r_dihedral_angle_3_deg 17.795 r_dihedral_angle_1_deg 6.105 r_angle_refined_deg 1.672 r_angle_other_deg 1.361 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7522 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 24
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling