2D6K

Crystal structure of mouse galectin-9 N-terminal CRD (crystal form 1)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.528915% ethanol, 0.1M CHES (pH9.5), VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5752.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.094α = 90
b = 58.094β = 90
c = 221.682γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0000Photon FactoryBL-6A

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
12.55099.90.0723514051
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)
2.52.591000.3527.3

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 REPLACEMENTTHROUGHOUTPDB entry 1A3K2.535.251328369699.990.208220.204460.28333RANDOM28.563
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]
0.140.14-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.912
r_dihedral_angle_3_deg16.869
r_dihedral_angle_4_deg14.985
r_dihedral_angle_1_deg7.885
r_scangle_it3.346
r_scbond_it2.129
r_angle_other_deg1.709
r_angle_refined_deg1.595
r_mcangle_it1.587
r_mcbond_it0.838
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.912
r_dihedral_angle_3_deg16.869
r_dihedral_angle_4_deg14.985
r_dihedral_angle_1_deg7.885
r_scangle_it3.346
r_scbond_it2.129
r_angle_other_deg1.709
r_angle_refined_deg1.595
r_mcangle_it1.587
r_mcbond_it0.838
r_symmetry_hbond_refined0.545
r_nbtor_refined0.318
r_nbd_refined0.205
r_symmetry_vdw_refined0.204
r_xyhbond_nbd_refined0.166
r_nbd_other0.142
r_nbtor_other0.119
r_chiral_restr0.112
r_mcbond_other0.067
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2352
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing