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Crystal structure of a computationally designed protein bound to a Mn-containing cofactor (L1-dnMSBP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 10YL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 700 uM L1-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 39.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.651 α = 90 b = 50.176 β = 90 c = 84.876 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 PILATUS3 6M 2022-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1 ALS 5.0.2
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 1.5 43.19 99.84 0.0713 0.07772 0.03046 0.999 11.44 6.3 32611 18.75
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 1.5 1.554 0.3799 0.4153 0.1656 0.918 0.95
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 1.5 43.19 1.35 32594 2965 99.29 0.1645 0.1629 0.1656 0.1979 0.2011 23.11
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 6.9874 f_angle_d 1.1634 f_chiral_restr 0.0613 f_bond_d 0.0114 f_plane_restr 0.0088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1677 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 41
Software Software Software Name Purpose BOS data collection xia2 data scaling xia2 data reduction PHENIX phasing PHENIX refinement