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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 3WP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 293 0.1 M HEPES-NaOH pH 8.6, 0.95 M ammonium sulfate and 0.1 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.38 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.427 α = 90 b = 207.281 β = 90 c = 100.784 γ = 90
Symmetry Space Group P 21 21 2
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 S 6M 2016-12-15 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) Rpim 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 1.9 47.62 99.9 0.107 0.045 0.997 12.9 6.7 141990 15.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.01 99.6 0.467 0.197 0.888 4.2 6.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3WP9 1.904 47.62 141916 7119 99.889 0.137 0.1366 0.1351 0.1641 0.1663 Random selection 19.482
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] -0.481 0.916 -0.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.994 r_dihedral_angle_3_deg 10.629 r_dihedral_angle_1_deg 7.204 r_lrange_it 6.661 r_lrange_other 6.147 r_scangle_it 4.535 r_scangle_other 4.534 r_dihedral_angle_4_deg 3.676 r_scbond_it 3.075 r_scbond_other 3.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.994 r_dihedral_angle_3_deg 10.629 r_dihedral_angle_1_deg 7.204 r_lrange_it 6.661 r_lrange_other 6.147 r_scangle_it 4.535 r_scangle_other 4.534 r_dihedral_angle_4_deg 3.676 r_scbond_it 3.075 r_scbond_other 3.074 r_mcangle_it 2.959 r_mcangle_other 2.959 r_mcbond_it 1.951 r_mcbond_other 1.947 r_angle_refined_deg 1.695 r_angle_other_deg 1.538 r_symmetry_xyhbond_nbd_refined 0.23 r_nbd_refined 0.204 r_symmetry_nbd_other 0.179 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.159 r_symmetry_nbd_refined 0.14 r_nbd_other 0.099 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8442 Nucleic Acid Atoms Solvent Atoms 1534 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing