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Protease structure from Euphorbia resinifera
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.2M sodium idodide (0.2 M), 0.1M Bis-Tris propane pH 8.5, 20% W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.87 57.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.673 α = 90 b = 112.88 β = 90 c = 201.801 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2018-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.7 64.16 99 0.116 0.141 0.08 0.995 9.7 5.8 168106
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 2.683 3.278 1.853 0.52 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.7 60.01 159344 8569 98.63 0.20434 0.20258 0.2143 0.23667 0.245 RANDOM 26.667
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] -0.33 1.98 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.678 r_dihedral_angle_4_deg 18.528 r_dihedral_angle_3_deg 13.99 r_dihedral_angle_1_deg 6.808 r_long_range_B_refined 5.429 r_long_range_B_other 5.392 r_scangle_other 4.461 r_mcangle_it 3.1 r_mcangle_other 3.1 r_scbond_it 2.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.678 r_dihedral_angle_4_deg 18.528 r_dihedral_angle_3_deg 13.99 r_dihedral_angle_1_deg 6.808 r_long_range_B_refined 5.429 r_long_range_B_other 5.392 r_scangle_other 4.461 r_mcangle_it 3.1 r_mcangle_other 3.1 r_scbond_it 2.997 r_scbond_other 2.997 r_mcbond_it 2.266 r_mcbond_other 2.266 r_angle_refined_deg 1.621 r_angle_other_deg 1.376 r_chiral_restr 0.076 r_bond_refined_d 0.01 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 9438 Nucleic Acid Atoms Solvent Atoms 701 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling HKL2Map phasing