☰ Navigation Tabs
Crystal structure of the Bowman-Birk inhibitor from snail medic seeds in complex with bovine trypsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D6R PDB ENTRY 1D6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 1.5M lithium sulphate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.47 α = 90 b = 54.47 β = 90 c = 180.08 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 MAR CCD 165 mm Mirrors: Three-segment Pt-coated toroidal 2004-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.00 ELETTRA 5.2R
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 2 30 95.8 0.093 4 2.4 34060 33730 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) 2 2.05 97.5 0.28 2.4 2.4 2479
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 (All) 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 1D6R 2 25 31992 31992 1680 95.62 0.2348 0.2348 0.23194 0.2302 0.28686 0.2807 RANDOM 29.668
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] 2.38 2.38 -4.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.597 r_dihedral_angle_3_deg 14.799 r_dihedral_angle_4_deg 12.559 r_dihedral_angle_1_deg 6.43 r_scangle_it 2.13 r_scbond_it 1.37 r_angle_refined_deg 1.356 r_mcangle_it 0.967 r_mcbond_it 0.552 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.597 r_dihedral_angle_3_deg 14.799 r_dihedral_angle_4_deg 12.559 r_dihedral_angle_1_deg 6.43 r_scangle_it 2.13 r_scbond_it 1.37 r_angle_refined_deg 1.356 r_mcangle_it 0.967 r_mcbond_it 0.552 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.249 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3669 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing