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Crystal structure of Ice binding protein from Candidatus Cryosericum odellii SMC5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 35% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.02 38.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.33 α = 90 b = 62.14 β = 93.746 c = 93.62 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 2023-12-26 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) 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 1.45 29.5 99.2 0.08 16.5 6.9 62809
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.53 99.2 0.32 6.5
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 1.45 29.5 62809 3124 98.764 0.152 0.1505 0.1505 0.1775 0.1773 8.967
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.748 r_dihedral_angle_4_deg 20.134 r_dihedral_angle_3_deg 9.534 r_dihedral_angle_1_deg 7.315 r_lrange_it 3.586 r_lrange_other 3.411 r_scangle_other 2.297 r_scangle_it 2.296 r_angle_refined_deg 1.781 r_scbond_it 1.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.748 r_dihedral_angle_4_deg 20.134 r_dihedral_angle_3_deg 9.534 r_dihedral_angle_1_deg 7.315 r_lrange_it 3.586 r_lrange_other 3.411 r_scangle_other 2.297 r_scangle_it 2.296 r_angle_refined_deg 1.781 r_scbond_it 1.707 r_scbond_other 1.705 r_angle_other_deg 1.569 r_mcangle_it 1.374 r_mcangle_other 1.374 r_mcbond_it 0.911 r_mcbond_other 0.911 r_symmetry_nbd_refined 0.265 r_nbd_refined 0.213 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.13 r_nbd_other 0.127 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3131 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing