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Crystal structure of engineered ice-binding protein (M74I and A97V) from Candidatus Cryosericum odellii strain SMC5_169
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9LHN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 90% of precipitant (35% PEG 2000 MME), 10% of mixture(6 M Ammonium nitrate, 0.1M Tris pH 8.5)
Crystal Properties Matthews coefficient Solvent content 1.97 37.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.15 α = 90 b = 61.92 β = 94.26 c = 92.54 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 9M 2024-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.453 29.352 99.51 0.03924 0.01636 0.999 28.83 6.6 61537
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.453 1.505 96.95 0.1599 0.07278 0.988 8.53 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.453 29.352 61537 3077 99.521 0.155 0.1535 0.1535 0.1816 0.1815 10.438
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] 0.001 -0.001 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.501 r_dihedral_angle_4_deg 15.454 r_dihedral_angle_3_deg 9.617 r_dihedral_angle_1_deg 7.545 r_lrange_it 3.529 r_lrange_other 3.313 r_scangle_other 2.258 r_scangle_it 2.256 r_angle_refined_deg 1.839 r_scbond_it 1.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.501 r_dihedral_angle_4_deg 15.454 r_dihedral_angle_3_deg 9.617 r_dihedral_angle_1_deg 7.545 r_lrange_it 3.529 r_lrange_other 3.313 r_scangle_other 2.258 r_scangle_it 2.256 r_angle_refined_deg 1.839 r_scbond_it 1.607 r_angle_other_deg 1.602 r_scbond_other 1.601 r_mcangle_it 1.357 r_mcangle_other 1.357 r_mcbond_it 0.951 r_mcbond_other 0.951 r_symmetry_nbd_refined 0.291 r_nbd_refined 0.212 r_nbd_other 0.211 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3117 Nucleic Acid Atoms Solvent Atoms 482 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing