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Crystal structure of fungal antifreeze protein with intermediate activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B5H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M Tris-HCl pH8.5, 30% (w/v) PEG 4000, 0.2M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.07 40.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.79 α = 90 b = 63.143 β = 90 c = 102.086 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 95 PIXEL DECTRIS EIGER X 4M 2019-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.7 49.68 99.8 0.192 0.201 0.057 0.98 8.6 12.9 41109
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 1.7 1.73 99.9 1.137 1.186 0.333 0.849 12.6
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 (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 5B5H 1.72 49.68 37745 1975 99.94 0.2103 0.2084 0.2227 0.2462 0.2551 RANDOM 10.893
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] -0.31 1.11 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.222 r_dihedral_angle_4_deg 10.931 r_dihedral_angle_3_deg 10.479 r_dihedral_angle_1_deg 7.819 r_angle_refined_deg 1.633 r_angle_other_deg 1.437 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.222 r_dihedral_angle_4_deg 10.931 r_dihedral_angle_3_deg 10.479 r_dihedral_angle_1_deg 7.819 r_angle_refined_deg 1.633 r_angle_other_deg 1.437 r_chiral_restr 0.072 r_bond_refined_d 0.01 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 3112 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 3
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction