7RD2

Co-crystal structure of Chaetomium glucosidase with compound 2


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
2.8957.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.563α = 90
b = 178.393β = 90
c = 179.677γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.9793APS23-ID-D

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
12.6146.6899.740.18050.0770.9857.966.565663
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)
12.612.70398.071.40.6180.5551.255.9

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 REPLACEMENTTHROUGHOUT7T6W2.6146.6862340334799.570.178760.176050.22891RANDOM52.427
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]
4.25-0.65-3.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.253
r_dihedral_angle_4_deg18.823
r_dihedral_angle_3_deg17.332
r_long_range_B_refined11.558
r_dihedral_angle_1_deg6.814
r_mcangle_it6.418
r_scbond_it6.359
r_mcbond_it4.437
r_angle_refined_deg1.597
r_chiral_restr0.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.253
r_dihedral_angle_4_deg18.823
r_dihedral_angle_3_deg17.332
r_long_range_B_refined11.558
r_dihedral_angle_1_deg6.814
r_mcangle_it6.418
r_scbond_it6.359
r_mcbond_it4.437
r_angle_refined_deg1.597
r_chiral_restr0.124
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12136
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms168

Software

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