8RMV

Galectin-3 with a bound inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NMN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M HEPES pH 7.5, 1.4 M Sodium citrate (Index/ B8)
Crystal Properties
Matthews coefficientSolvent content
1.9135.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.34α = 90
b = 57.66β = 90
c = 61.11γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2020-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.9998SLSX06DA

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
11.1541.93899.20.0590.9999.042.5582647
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)
11.151.2298.51.2070.4032.7

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-VALUE1.3541.90427362136999.9560.160.15830.17060.18350.187416.037
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]
-1.08-0.9952.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.182
r_dihedral_angle_3_deg12.12
r_lrange_it10.447
r_lrange_other10.446
r_dihedral_angle_1_deg7.612
r_scangle_it5.821
r_scangle_other5.815
r_dihedral_angle_2_deg4.589
r_mcangle_it3.996
r_mcangle_other3.996
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.182
r_dihedral_angle_3_deg12.12
r_lrange_it10.447
r_lrange_other10.446
r_dihedral_angle_1_deg7.612
r_scangle_it5.821
r_scangle_other5.815
r_dihedral_angle_2_deg4.589
r_mcangle_it3.996
r_mcangle_other3.996
r_scbond_it3.831
r_scbond_other3.819
r_mcbond_it2.679
r_mcbond_other2.666
r_rigid_bond_restr1.603
r_angle_refined_deg1.221
r_chiral_restr_other0.888
r_angle_other_deg0.665
r_symmetry_nbd_refined0.205
r_symmetry_nbd_other0.195
r_nbd_refined0.184
r_nbtor_refined0.167
r_nbd_other0.159
r_symmetry_xyhbond_nbd_refined0.141
r_xyhbond_nbd_refined0.108
r_symmetry_nbtor_other0.083
r_chiral_restr0.064
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1093
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing