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The crystal structure of Nattokinase fragments
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DWW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 288 0.1M HEPES ,0.8 M Potassium sodium tartrate tetrahydrate
Crystal Properties Matthews coefficient Solvent content 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.284 α = 90 b = 73.959 β = 97.47 c = 67.811 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARMOSAIC 225 mm CCD 2016-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.987 SSRF BL17U
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 1.77 50 99.6 12.4 7.2 49947
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 4dww 1.8 50 45026 2344 99.62 0.23363 0.23067 0.2442 0.29053 0.3047 RANDOM 9.761
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] 0.83 -1.05 -0.46 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.516 r_dihedral_angle_4_deg 16.471 r_dihedral_angle_3_deg 15.518 r_dihedral_angle_1_deg 6.513 r_long_range_B_refined 3.633 r_long_range_B_other 3.062 r_angle_refined_deg 1.935 r_scangle_other 1.541 r_mcangle_it 1.062 r_mcangle_other 1.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.516 r_dihedral_angle_4_deg 16.471 r_dihedral_angle_3_deg 15.518 r_dihedral_angle_1_deg 6.513 r_long_range_B_refined 3.633 r_long_range_B_other 3.062 r_angle_refined_deg 1.935 r_scangle_other 1.541 r_mcangle_it 1.062 r_mcangle_other 1.061 r_scbond_it 1.004 r_scbond_other 1.004 r_angle_other_deg 0.993 r_mcbond_it 0.677 r_mcbond_other 0.672 r_chiral_restr 0.116 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3904 Nucleic Acid Atoms Solvent Atoms 758 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing