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Crystal structure of an ice-binding protein (FfIBP) from the Antarctic bacterium, Flavobacterium frigoris PS1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 293 0.1M sodium acetate, 3M sodium chloride, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.2 70.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.171 α = 90 b = 69.171 β = 90 c = 178.764 γ = 90
Symmetry Space Group P 41 2 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 CCD ADSC QUANTUM 315r 2012-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9795 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 37.81 97.8 25048 24497 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 99.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 THROUGHOUT 3UYU 2.1 37.81 1 25048 24497 1309 97.83 0.2193 0.21005 0.20848 0.2132 0.23901 0.2419 RANDOM 41.85
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 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.293 r_dihedral_angle_4_deg 16.66 r_dihedral_angle_3_deg 15.079 r_long_range_B_refined 7.438 r_long_range_B_other 7.414 r_scangle_other 6.805 r_dihedral_angle_1_deg 6.582 r_mcangle_other 4.879 r_mcangle_it 4.864 r_scbond_it 4.729
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.293 r_dihedral_angle_4_deg 16.66 r_dihedral_angle_3_deg 15.079 r_long_range_B_refined 7.438 r_long_range_B_other 7.414 r_scangle_other 6.805 r_dihedral_angle_1_deg 6.582 r_mcangle_other 4.879 r_mcangle_it 4.864 r_scbond_it 4.729 r_scbond_other 4.726 r_mcbond_it 4.151 r_mcbond_other 4.127 r_angle_refined_deg 2.047 r_angle_other_deg 0.97 r_chiral_restr 0.129 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 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 1554 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling