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Structure of the type III fish antifreeze protein from Zoarces viviparus ZvAFP6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OPS PDB ENTRY 1OPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2.5 M (NH4)2SO4, 0.1 M CITRIC ACID, PH 4
Crystal Properties Matthews coefficient Solvent content 2.84 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.57 α = 90 b = 108.17 β = 90 c = 38.25 γ = 90
Symmetry Space Group C 2 2 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 CCD MARRESEARCH 2009-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
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 1.2 30 98.5 0.03 25.2 6.2 300182 -3
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 1.2 1.23 94.9 0.43 5.2 5
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 PDB ENTRY 1OPS 1.2 61.9 46138 2463 98.49 0.17965 0.17884 0.1725 0.19536 0.1896 RANDOM 24.805
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] 0.14 -0.34 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.54 r_dihedral_angle_3_deg 10.44 r_sphericity_free 9.801 r_sphericity_bonded 7.178 r_dihedral_angle_1_deg 5.654 r_scangle_it 5.359 r_scbond_it 3.994 r_mcangle_it 2.847 r_rigid_bond_restr 2.386 r_mcbond_it 2.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.54 r_dihedral_angle_3_deg 10.44 r_sphericity_free 9.801 r_sphericity_bonded 7.178 r_dihedral_angle_1_deg 5.654 r_scangle_it 5.359 r_scbond_it 3.994 r_mcangle_it 2.847 r_rigid_bond_restr 2.386 r_mcbond_it 2.122 r_angle_refined_deg 1.819 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.284 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.121 r_symmetry_hbond_refined 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 912 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing