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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 VAPOR DIFFUSION, HANGING DROP , pH 6, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.02 39.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.734 α = 90 b = 56.096 β = 90 c = 70.764 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 2.29
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 2.2 90 99.2 0.071 41.2 11.9 10270 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) 2.2 2.29 92.3 0.216 5.1 7.9 932
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.2 29.93 10129 1004 98.23 0.1785 0.172 0.2392 0.2608 RANDOM 22.5708
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] 0.69 -0.34 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.679 r_dihedral_angle_4_deg 18.458 r_dihedral_angle_3_deg 14.406 r_dihedral_angle_1_deg 5.435 r_angle_refined_deg 1.066 r_nbtor_refined 0.299 r_metal_ion_refined 0.255 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.185 r_xyhbond_nbd_refined 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.679 r_dihedral_angle_4_deg 18.458 r_dihedral_angle_3_deg 14.406 r_dihedral_angle_1_deg 5.435 r_angle_refined_deg 1.066 r_nbtor_refined 0.299 r_metal_ion_refined 0.255 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.185 r_xyhbond_nbd_refined 0.118 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1688 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 5
Software Software Software Name Purpose SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection DENZO data reduction SCALEPACK data scaling