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Structure of the type III fish antifreeze protein from Zoarces viviparus ZvAFP13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MSI PDB ENTRY 4MSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2.5 M (NH4)2SO4, 0.1 M CITRIC ACID, PH 4.5
Crystal Properties Matthews coefficient Solvent content 1.99 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.26 α = 90 b = 39.69 β = 90 c = 44.22 γ = 90
Symmetry Space Group P 21 21 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 2009-04-30 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 1.45 29.54 98 0.04 24.2 4.4 10321 -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 1.45 1.49 92.5 0.31 4.7 3.4
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 4MSI 1.45 29.54 9826 494 98.03 0.13583 0.13379 0.1304 0.17588 0.1759 RANDOM 15.88
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] -0.13 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.846 r_sphericity_free 24.386 r_dihedral_angle_4_deg 23.352 r_dihedral_angle_3_deg 14.579 r_sphericity_bonded 12.23 r_dihedral_angle_1_deg 5.657 r_rigid_bond_restr 4.083 r_angle_refined_deg 1.864 r_chiral_restr 0.113 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.846 r_sphericity_free 24.386 r_dihedral_angle_4_deg 23.352 r_dihedral_angle_3_deg 14.579 r_sphericity_bonded 12.23 r_dihedral_angle_1_deg 5.657 r_rigid_bond_restr 4.083 r_angle_refined_deg 1.864 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 481 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing