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Structure of RvY_06210 at 1.05 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Structure determined by SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Magnesium chloride hexahydrate, 0.03M Tris-HCl pH8.2 , 19% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.87 34.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.362 α = 90 b = 64.02 β = 109.54 c = 45.987 γ = 90
Symmetry Space Group C 1 2 1
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) 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 1.05 37.02 95.8 0.039 0.046 0.025 0.998 14.9 3.4 108442 10.22
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 1.05 1.07 0.576 0.676 0.352 0.76 1.8
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 1.05 37.02 1.38 108435 5426 95.52 0.1299 0.1286 0.1379 0.1545 0.1586 19.28
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 13.2213 f_angle_d 0.8934 f_chiral_restr 0.0686 f_plane_restr 0.009 f_bond_d 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1999 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing