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the DISMED2 domain of RetS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JYB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 0.1M BIs-Tris Propane pH 8.5, 0.2 M NaI, 20% peg3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.582 α = 90 b = 80.582 β = 90 c = 51.349 γ = 90
Symmetry Space Group P 43 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 PILATUS3 6M 2024-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97946 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.5 50 97.12 0.917 2.68 7.6 39591 82.73
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 3.5 4.4 97.8 0.64 1.11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3JYB 3.5 43.3 1.34 2290 230 97.12 0.2762 0.2714 0.2711 0.3258 0.3196 91.6
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 13.7447 f_angle_d 0.9483 f_chiral_restr 0.0538 f_plane_restr 0.0109 f_bond_d 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1149 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing