8RRE

Galectin-3 with a small molecule inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherIn-house unliganded structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2932.1 M DL-Malic acid pH 7.0
Crystal Properties
Matthews coefficientSolvent content
1.9637.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.518α = 90
b = 57.531β = 90
c = 62.116γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2021-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.20842.20998.90.9990.0832.9472732
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.2081.282.20.1850.58

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.20842.20838490190699.4270.1580.15610.16580.18820.194416.881
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]
-1.7570.2171.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.128
r_lrange_it12.927
r_lrange_other12.088
r_dihedral_angle_3_deg11.947
r_scangle_it9.298
r_scangle_other9.29
r_dihedral_angle_1_deg7.279
r_scbond_it6.454
r_scbond_other6.441
r_mcangle_other6.368
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.128
r_lrange_it12.927
r_lrange_other12.088
r_dihedral_angle_3_deg11.947
r_scangle_it9.298
r_scangle_other9.29
r_dihedral_angle_1_deg7.279
r_scbond_it6.454
r_scbond_other6.441
r_mcangle_other6.368
r_mcangle_it6.367
r_dihedral_angle_2_deg6.343
r_mcbond_it4.503
r_mcbond_other4.492
r_rigid_bond_restr3.711
r_angle_refined_deg1.65
r_angle_other_deg0.631
r_nbd_refined0.21
r_symmetry_nbd_other0.195
r_symmetry_nbd_refined0.189
r_nbtor_refined0.171
r_symmetry_xyhbond_nbd_refined0.171
r_xyhbond_nbd_refined0.155
r_nbd_other0.154
r_chiral_restr0.092
r_symmetry_nbtor_other0.085
r_chiral_restr_other0.017
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1105
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing