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Crystal structure of Q40A mutant of a computationally designed protein bound to a Mn-containing cofactor (L1-Q40A-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-Q40A-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 2.07 40.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.925 α = 90 b = 50.517 β = 90 c = 84.771 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 2023-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 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 1.62 43.4 99.98 0.1172 0.1279 0.05049 0.996 8.46 6.4 26287 19.36
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 1.62 1.678 0.701 0.7623 0.2968 0.721 1.06
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 1.62 43.4 1.37 26284 2363 99.88 0.1812 0.1792 0.1792 0.2224 0.2214 21.38
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 6.1058 f_angle_d 0.748 f_chiral_restr 0.0379 f_plane_restr 0.0074 f_bond_d 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1677 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 41
Software Software Software Name Purpose JBluIce-EPICS data collection xia2 data scaling xia2 data reduction PHENIX phasing PHENIX refinement