8RR8

Galectin-3 with a small molecule inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherInternal structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2932.1 M DL-Malic acid pH 7.0
Crystal Properties
Matthews coefficientSolvent content
1.9536.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.5α = 90
b = 57.34β = 90
c = 61.95γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2022-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.542.08199.70.0810.9988.663.4637873
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)
11.51.592.020.2570.65

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-VALUE1.530.99420294103899.9260.1680.1660.17330.21630.230725.62
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]
-2.4153.498-1.083
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it15.736
r_lrange_other15.587
r_dihedral_angle_6_deg14.57
r_dihedral_angle_3_deg13.284
r_scangle_it12.931
r_scangle_other12.924
r_scbond_it9.385
r_scbond_other9.378
r_mcangle_other9.356
r_mcangle_it9.355
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it15.736
r_lrange_other15.587
r_dihedral_angle_6_deg14.57
r_dihedral_angle_3_deg13.284
r_scangle_it12.931
r_scangle_other12.924
r_scbond_it9.385
r_scbond_other9.378
r_mcangle_other9.356
r_mcangle_it9.355
r_dihedral_angle_1_deg7.737
r_mcbond_it7.222
r_mcbond_other7.203
r_dihedral_angle_2_deg5.552
r_rigid_bond_restr4.23
r_chiral_restr_other1.685
r_angle_refined_deg1.653
r_angle_other_deg0.585
r_nbd_refined0.195
r_symmetry_nbd_other0.195
r_nbd_other0.187
r_nbtor_refined0.166
r_symmetry_nbd_refined0.166
r_xyhbond_nbd_refined0.134
r_symmetry_xyhbond_nbd_refined0.132
r_symmetry_nbtor_other0.083
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1108
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing