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Crystal structure of V30M-TTR in complex with compound 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PWE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 400, sodium acetate, calcium chloride
Crystal Properties Matthews coefficient Solvent content 1.71 27.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.536 α = 90 b = 85.273 β = 90 c = 63.79 γ = 90
Symmetry Space Group P 21 21 2
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-F 2021-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.696 42.64 97.3 0.116 0.04 0.995 13.7 7.6 26271
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 92.6 0.558 0.213 0.896 5.5
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 1.696 25.54 1.36 26262 1313 97.22 0.2041 0.2027 0.2047 0.2309 0.235
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 19.818 f_angle_d 1.062 f_chiral_restr 0.086 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1771 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing