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Crystal structure of L8Q mutant of a computationally designed protein bound to a Mn-containing cofactor (L1-L8Q-dnMSBP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 10YM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 700 uM L1-L8Q-dnMSBP in 25 mM Tris buffer at pH 8 containing 300 mM NaCl was mixed with 20 mM ammonium phosphate monobasic buffer at pH 4.0 with 11-16% w/v PEG 3350 at a 1.5 uL : 1.5 uL mixing ratio under room temperature.
Crystal Properties Matthews coefficient Solvent content 2.04 39.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.377 α = 90 b = 50.08 β = 90 c = 85.464 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 2023-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03317 APS 23-ID-B
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 1.78 34.03 99.95 0.1074 0.1156 0.04221 0.998 12.08 7.3 19695 23.84
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 1.78 1.844 0.8903 0.9646 0.3663 0.815 1.13
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 1.78 34.03 1.35 19690 1879 99.92 0.1704 0.1681 0.1696 0.216 0.2126 24.84
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 6.718 f_angle_d 0.8211 f_chiral_restr 0.0437 f_plane_restr 0.0067 f_bond_d 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1664 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 41
Software Software Software Name Purpose JBluIce-EPICS data collection xia2 data scaling xia2 data reduction PHENIX phasing PHENIX refinement