6A8K

Crystal structure of Ice-binding Protein from a Sea-Ice Microalga


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.1M Tris-HCl pH8.5, 2.0M Ammonium dihydrogen phosphate
Crystal Properties
Matthews coefficientSolvent content
2.2244.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.054α = 90
b = 47.586β = 90
c = 134.517γ = 90
Symmetry
Space GroupP 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95PIXELDECTRIS PILATUS3 6M2015-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9800Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.447.699.70.05724.112.346394
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4898.70.4346.311.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3VN31.447.5944028231999.560.138060.13680.1622RANDOM15.013
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]
1.09-0.92-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.51
r_dihedral_angle_4_deg11.792
r_dihedral_angle_3_deg9.913
r_dihedral_angle_1_deg7.045
r_long_range_B_other5.749
r_long_range_B_refined5.748
r_scangle_other4.052
r_scbond_it2.856
r_scbond_other2.844
r_mcangle_it2.506
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.51
r_dihedral_angle_4_deg11.792
r_dihedral_angle_3_deg9.913
r_dihedral_angle_1_deg7.045
r_long_range_B_other5.749
r_long_range_B_refined5.748
r_scangle_other4.052
r_scbond_it2.856
r_scbond_other2.844
r_mcangle_it2.506
r_mcangle_other2.506
r_angle_refined_deg2.478
r_mcbond_it1.72
r_mcbond_other1.72
r_angle_other_deg1.153
r_chiral_restr0.139
r_bond_refined_d0.029
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms1725
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing