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Nanorana parkeri saxiphilin:GTX5 (co-crystal)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8D6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277.15 20-25% v/v PEG400, 4-5% w/v PGA-LM, 100-200 mM sodium acetate, pH 5.0, GTX5:NpSxph molar ratio 1.2:1
Crystal Properties Matthews coefficient Solvent content 3.6 65.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 229.156 α = 90 b = 229.156 β = 90 c = 67.505 γ = 120
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 PILATUS 6M 2022-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11614 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 43.31 99.98 0.1362 0.998 8.15 15.1 104167
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.968 99.99 0.58 1.19
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 THROUGHOUT 1.9 43.31 1.96 104157 2004 99.99 0.1903 0.1898 0.1906 0.2181 0.2193
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 8.406 f_angle_d 0.892 f_chiral_restr 0.056 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6382 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction PHASER phasing XDS data reduction