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Structure of a type III antifreeze protein isoform HPLC12 re-refined using standard protocols
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.27 α = 90 b = 39.89 β = 90 c = 44.54 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 295 IMAGE PLATE MARRESEARCH 1996-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 8 99.1 0.077 7.8 3.8 4933 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 98.3 0.306
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.9 8 4637 262 98.95 0.15215 0.15001 0.1628 0.18908 0.1962 RANDOM 19.29
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.077 r_dihedral_angle_4_deg 25.014 r_dihedral_angle_3_deg 14.206 r_long_range_B_other 7.342 r_long_range_B_refined 7.298 r_dihedral_angle_1_deg 6.307 r_scangle_other 5.585 r_scbond_it 3.549 r_scbond_other 3.529 r_mcangle_other 3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.077 r_dihedral_angle_4_deg 25.014 r_dihedral_angle_3_deg 14.206 r_long_range_B_other 7.342 r_long_range_B_refined 7.298 r_dihedral_angle_1_deg 6.307 r_scangle_other 5.585 r_scbond_it 3.549 r_scbond_other 3.529 r_mcangle_other 3 r_mcangle_it 2.976 r_mcbond_it 1.868 r_mcbond_other 1.83 r_angle_refined_deg 1.751 r_angle_other_deg 1.334 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 491 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing