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Structure of SPCC1393.13 protein from fission yeast
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7T7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.24 mM SPCC1393.13 protein in a buffer containing 5 mM CoCl2, 10 mM sodium pyrophosphate (pH 6.5), 18 mM Tris-HCl (pH 7.5), and 135 mM NaCl mixed with precipitant solution containing 0.1 M citric acid (pH 5.0) and 20% (w/v) PEG-6000
Crystal Properties Matthews coefficient Solvent content 2.59 52.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.72 α = 90 b = 88.221 β = 101.067 c = 48.257 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 EIGER2 X 16M 2021-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.5895 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.99 47.36 90.5 0.048 0.995 12.7 6.1 31632 18.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.05 0.311 0.797 2.8
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 7T7K 2 47.36 1.34 31625 3062 89.16 0.1621 0.16 0.16 0.2003 0.2022 29.11
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 6.9475 f_angle_d 0.9875 f_chiral_restr 0.0584 f_bond_d 0.0083 f_plane_restr 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3530 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing