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Crystal Structure of the Snow Flea Antifreeze Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BOG PDB entry 3BOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 296 pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 1.65 25.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 16.699 α = 90 b = 74.281 β = 102.2 c = 17.687 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 CCD 2006-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 0.95 50 90.6 0.059 17.9 3.3 23972 -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) 0.95 0.98 46 0.25 3 1.3
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 3BOG 0.98 17.29 21783 1173 95.5 0.141 0.14 0.1466 0.164 0.1758 RANDOM 6.59
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] 0.11 0.79 -0.79 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.41 r_dihedral_angle_4_deg 12.307 r_dihedral_angle_3_deg 10.983 r_sphericity_free 9.026 r_dihedral_angle_1_deg 7.229 r_sphericity_bonded 4.616 r_scangle_it 3.541 r_scbond_it 2.685 r_mcangle_it 1.938 r_angle_refined_deg 1.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.41 r_dihedral_angle_4_deg 12.307 r_dihedral_angle_3_deg 10.983 r_sphericity_free 9.026 r_dihedral_angle_1_deg 7.229 r_sphericity_bonded 4.616 r_scangle_it 3.541 r_scbond_it 2.685 r_mcangle_it 1.938 r_angle_refined_deg 1.674 r_mcbond_it 1.429 r_rigid_bond_restr 1.34 r_mcbond_other 1.147 r_angle_other_deg 0.865 r_symmetry_vdw_other 0.212 r_nbd_refined 0.198 r_nbd_other 0.183 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.16 r_symmetry_vdw_refined 0.156 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.112 r_nbtor_other 0.083 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 453 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing