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Crystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28 nm resolution. Structural peculiarities in a folded protein conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PI2 PDB ENTRY 1PI2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 289 PEG 4000, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, SITTING DROP at 289K
Crystal Properties Matthews coefficient Solvent content 4.13 70.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.1 α = 90 b = 86.1 β = 90 c = 86.1 γ = 90
Symmetry Space Group P 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 DIFFRACTOMETER WEISSENBERG 1994-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.04 Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 60.9 96.3 0.058 0.058 6.88 3891 26756 -3
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) 2.8 3 70 0.3
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PI2 2.8 8 2 2722 2450 272 96.3 0.221 0.308 random 28.7
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 29.7 x_improper_angle_d 2.8 x_angle_deg 1.6 x_bond_d 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 513 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms
Software Software Software Name Purpose WEIS data scaling ROTAVATA data reduction X-PLOR model building X-PLOR refinement WEIS data reduction CCP4 data scaling ROTAVATA data scaling X-PLOR phasing