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Actinidin from Actinidia arguta planch (Sarusashi)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 288 30% PEG 400, 0.1M sodium acetate, 30mM Cadmium chloride , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 1.93 36.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.269 α = 90 b = 55.812 β = 90 c = 70.225 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 IMAGE PLATE RIGAKU RAXIS VII Mirrors 2008-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.54
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 1.9 90 99.8 0.083 41.3 12.8 15226 2
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) 1.9 1.97 100 0.275 6.1 13 1494
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 1.9 19.64 15163 1528 99.8 0.169 0.1642 0.166 0.2129 0.2166 RANDOM 20.6068
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] 1.59 -0.85 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.796 r_dihedral_angle_4_deg 16.932 r_dihedral_angle_3_deg 13.041 r_dihedral_angle_1_deg 5.277 r_scangle_it 1.689 r_scbond_it 1.142 r_angle_refined_deg 0.983 r_mcangle_it 0.765 r_mcbond_it 0.439 r_metal_ion_refined 0.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.796 r_dihedral_angle_4_deg 16.932 r_dihedral_angle_3_deg 13.041 r_dihedral_angle_1_deg 5.277 r_scangle_it 1.689 r_scbond_it 1.142 r_angle_refined_deg 0.983 r_mcangle_it 0.765 r_mcbond_it 0.439 r_metal_ion_refined 0.336 r_nbtor_refined 0.302 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.117 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1689 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 9
Software Software Software Name Purpose SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection DENZO data reduction SCALEPACK data scaling