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Structure of human COQ9 protein with bound isoprene.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 293 Crystals were grown by seeded micro batch in a glass depression plate, on glass coverslips. The experiment was sealed with FOMBLIN oil. 2 microliters of protein saturated with geranylgeraniol was mixed with 1 microliter of seed stock and two microliters of reservoir solution. The reservoir solution was composed of 1.2 molar ammonium sulfate and 0.1 molar TrisHCl buffer at pH 8.5. The reservoir was saturated with geranylgeraniol by adding several microliters of neat geranylgeraniol.
Crystal Properties Matthews coefficient Solvent content 2.91 57.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.45 α = 90 b = 222.78 β = 90 c = 130.78 γ = 90
Symmetry Space Group C 2 2 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 9M 2017-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.127230 APS 21-ID-D
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 2 48 99.68 0.1274 0.1325 0.03598 0.998 15.48 13.5 114146 37.83
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 2 2.07 99.87 1.759 1.824 0.4802 0.622 1.51 14.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6AWL 2 48 1.34 114139 2045 99.69 0.17 0.1693 0.1768 0.2094 0.2144 thin shells
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 11.105 f_angle_d 1.357 f_chiral_restr 0.076 f_bond_d 0.019 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9128 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing