8ER4

Co-crystal structure of Chaetomium glucosidase with compound 23


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7T6W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52970.1 Bis Tris pH 6.5, 1.6-2.0 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.9458.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.653α = 90
b = 177.198β = 90
c = 180.176γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.033APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
12.346.897.510.087470.03120.99713.978.896056
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3892.960.59980.20780.9162.46

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 REPLACEMENTTHROUGHOUT7T6W2.346.891349469899.010.19980.19750.2463RANDOM43.007
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]
2.430.19-2.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.458
r_dihedral_angle_4_deg17.631
r_dihedral_angle_3_deg16.527
r_dihedral_angle_1_deg7.557
r_angle_refined_deg1.592
r_angle_other_deg1.335
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.458
r_dihedral_angle_4_deg17.631
r_dihedral_angle_3_deg16.527
r_dihedral_angle_1_deg7.557
r_angle_refined_deg1.592
r_angle_other_deg1.335
r_chiral_restr0.078
r_bond_refined_d0.009
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 Atoms12024
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms164

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing