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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 9LHN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium cacodylate pH 5.0, 0.2 M Sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.75 α = 90 b = 47.56 β = 92.222 c = 66.77 γ = 90
Symmetry Space Group C 1 2 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 1.8 29.394 98.6 0.04 25.6 6.9 63299
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 1.8 1.84 0.18
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 1.8 29.394 63298 3189 98.293 0.165 0.1631 0.1743 0.2051 0.2131 17.116
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] 0.002 -0.003 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.706 r_dihedral_angle_4_deg 15.4 r_dihedral_angle_3_deg 10.077 r_dihedral_angle_1_deg 7.398 r_lrange_it 4.142 r_lrange_other 3.897 r_scangle_it 2.777 r_scangle_other 2.776 r_scbond_it 1.871 r_scbond_other 1.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.706 r_dihedral_angle_4_deg 15.4 r_dihedral_angle_3_deg 10.077 r_dihedral_angle_1_deg 7.398 r_lrange_it 4.142 r_lrange_other 3.897 r_scangle_it 2.777 r_scangle_other 2.776 r_scbond_it 1.871 r_scbond_other 1.871 r_mcangle_it 1.834 r_mcangle_other 1.834 r_angle_refined_deg 1.674 r_angle_other_deg 1.433 r_mcbond_it 1.374 r_mcbond_other 1.363 r_symmetry_nbd_other 0.191 r_nbd_refined 0.189 r_symmetry_nbd_refined 0.159 r_nbtor_refined 0.157 r_nbd_other 0.15 r_xyhbond_nbd_refined 0.132 r_symmetry_xyhbond_nbd_refined 0.108 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4802 Nucleic Acid Atoms Solvent Atoms 760 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing