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Crystal structure of calotropain FI from Calotropis gigantea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 9 293 0.1 M TBG (Tartrate, Bis-Tris, Glycylglycin) buffer pH 6.0 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.77 55.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.616 α = 90 b = 121.272 β = 90 c = 61.006 γ = 90
Symmetry Space Group C 2 2 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 CCD MARMOSAIC 225 mm CCD Mirror 2021-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97893 RRCAT INDUS-2 PX-BL21
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 1.25 43.01 98.1 0.069 0.072 0.02 0.999 19.9 12.1 68894 14.26
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 1.25 1.27 76.8 0.464 0.535 0.257 0.826 1.7 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.25 43.01 1.36 68894 3387 98.09 0.1657 0.1648 0.1656 0.1842 0.1849 20.46
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.1006 f_angle_d 1.2401 f_chiral_restr 0.1059 f_bond_d 0.0128 f_plane_restr 0.0112
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1639 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing RESOLVE model building Coot model building