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Crystal structure of Dionain-1, the major endopeptidase in the Venus flytrap digestive juice
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S4V PDB ENTRY 1S4V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 DI-POTASSIUM HYDROGEN PHOSPHATE 0.8 M, SODIUM DIHYDROGEN PHOSPHATE 0.9 M, LITHIUM SULFATE ANHYDROUS 0.2 M, CAPS 0.1 M, PH 10.5
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.85 α = 90 b = 47.79 β = 92.44 c = 57.79 γ = 90
Symmetry Space Group C 1 2 1
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 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.5 40.1 94.9 0.03 30.7 3.1 30734 2 15.44
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 1.5 1.7 94.8 0.09 16 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1S4V 1.5 13.27 30697 774 95 0.1579 0.1575 0.172 0.1913 RANDOM 19.55
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] -0.035 -2.2552 0.0827 -0.0476
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.01 t_other_torsion 2.46 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.01 t_other_torsion 2.46 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1616 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 23
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing