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Structure of RvY_06210 at 1.45 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other preliminary structure determined by SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.4M Sodium thiocyanate, 0.1M Sodium acetate pH4.0, 16% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.74 55.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.96 α = 90 b = 82.161 β = 90 c = 145.065 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 PIXEL DECTRIS EIGER X 16M 2022-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.45 48.96 99.8 0.059 0.064 0.999 16.1 6.7 129382 19.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 1.32 1.431 0.586
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 1.45 40.58 1.35 129284 6473 99.8 0.169 0.1677 0.1678 0.1922 0.192 24.62
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 5.9319 f_angle_d 0.8419 f_chiral_restr 0.0719 f_plane_restr 0.0075 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4092 Nucleic Acid Atoms Solvent Atoms 910 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing