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Crystal structure of ice-binding protein from an Antarctic ascomycete, Antarctomyces psychrotrophicus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M Bis-Tris pH 7.0, 4.0 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 4.09 69.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.311 α = 90 b = 92.311 β = 90 c = 222.669 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS3 2M 2018-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.02 46.16 99.9 0.082 0.085 1 21.1 19.8 72989
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.06 99.8 1.654 1.698 0.382 0.944 2.2 19.6
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 (All) 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 FREE R-VALUE 7BWX 2.02 45.725 72904 3649 99.874 0.181 0.1808 0.1789 0.179 0.2157 0.2157 Random selection 56.926
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] 0.014 0.007 0.014 -0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.863 r_dihedral_angle_3_deg 12.32 r_lrange_it 8.943 r_scangle_it 8.104 r_dihedral_angle_1_deg 7.912 r_scbond_it 7.257 r_mcangle_it 7.096 r_mcbond_it 5.842 r_dihedral_angle_4_deg 3.136 r_angle_refined_deg 2.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.863 r_dihedral_angle_3_deg 12.32 r_lrange_it 8.943 r_scangle_it 8.104 r_dihedral_angle_1_deg 7.912 r_scbond_it 7.257 r_mcangle_it 7.096 r_mcbond_it 5.842 r_dihedral_angle_4_deg 3.136 r_angle_refined_deg 2.081 r_nbtor_refined 0.327 r_symmetry_nbd_refined 0.276 r_nbd_refined 0.216 r_chiral_restr 0.144 r_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.141 r_gen_planes_refined 0.012 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4239 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing