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Hydrophobic ice-binding site confer hyperactivity on antifreeze protein from a snow mold fungus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES monohydrate, 1.6 M ammonium sulfate, 10%(v/v) 1,4-dioxane
Crystal Properties Matthews coefficient Solvent content 1.92 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.388 α = 90 b = 104.849 β = 90 c = 35.626 γ = 90
Symmetry Space Group P 21 21 2
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 2014-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98000 Photon Factory BL-17A
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 52.4 84.5 0.091 4.8 10.5 83006
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 1.06 24.6 0.419 1.5 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3VN3 1 52.4 78830 4093 84.38 0.12098 0.1202 0.1206 0.13578 0.1361 RANDOM 10.809
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] 0.06 -0.32 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.321 r_sphericity_free 28.557 r_rigid_bond_restr 11.361 r_dihedral_angle_3_deg 9.657 r_sphericity_bonded 9.541 r_dihedral_angle_1_deg 7.001 r_dihedral_angle_4_deg 5.184 r_long_range_B_refined 3.277 r_scbond_it 2.447 r_angle_refined_deg 2.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.321 r_sphericity_free 28.557 r_rigid_bond_restr 11.361 r_dihedral_angle_3_deg 9.657 r_sphericity_bonded 9.541 r_dihedral_angle_1_deg 7.001 r_dihedral_angle_4_deg 5.184 r_long_range_B_refined 3.277 r_scbond_it 2.447 r_angle_refined_deg 2.269 r_mcangle_it 0.951 r_mcbond_it 0.8 r_chiral_restr 0.15 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1559 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing