8OZ1

CjCel5D endo-xyloglucanase bounc to CB665 covalent inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OYC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429320 mg/mL enzyme in 50 mM NaPi pH 7.0 mixed 1:1 with 0.1 M MIB buffer, pH 4, 25% PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.244.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.36α = 90
b = 57.132β = 98.528
c = 65.951γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.351.7897.20.1490.0440.9978.311.391883
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)
11.31.3275.31.1130.5420.5770.95

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.351.7891862453797.1030.1360.13440.1691Random selection16.393
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]
0.8880.919-1.6440.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.515
r_dihedral_angle_3_deg14.464
r_dihedral_angle_1_deg6.916
r_dihedral_angle_2_deg5.304
r_rigid_bond_restr4.329
r_lrange_it3.931
r_lrange_other3.689
r_scangle_it3.182
r_scangle_other3.182
r_mcangle_other2.622
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.515
r_dihedral_angle_3_deg14.464
r_dihedral_angle_1_deg6.916
r_dihedral_angle_2_deg5.304
r_rigid_bond_restr4.329
r_lrange_it3.931
r_lrange_other3.689
r_scangle_it3.182
r_scangle_other3.182
r_mcangle_other2.622
r_mcangle_it2.61
r_scbond_it2.503
r_scbond_other2.503
r_mcbond_it2.084
r_mcbond_other2.084
r_angle_refined_deg1.741
r_angle_other_deg0.733
r_symmetry_xyhbond_nbd_refined0.282
r_nbd_refined0.271
r_symmetry_nbd_other0.218
r_nbtor_refined0.183
r_nbd_other0.165
r_xyhbond_nbd_refined0.147
r_symmetry_nbd_refined0.118
r_chiral_restr0.093
r_symmetry_nbtor_other0.075
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.008
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2954
Nucleic Acid Atoms
Solvent Atoms424
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing