5GLY

Crystal structure of a glycoside hydrolase in complex with cellotetrose from Thielavia terrestris NRRL 8126


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OA7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298MgCl2, Tris-Cl, PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.5251.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.342α = 90
b = 54.793β = 90
c = 84.839γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.0NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.582599.70.04530.65.331570
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.6499.20.1870.9875.3

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 REPLACEMENTTHROUGHOUT1OA71.582529867162299.650.15340.15190.18RANDOM18.875
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]
2.01-0.79-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.068
r_dihedral_angle_3_deg11.765
r_dihedral_angle_4_deg8.066
r_dihedral_angle_1_deg7.553
r_mcangle_it2.674
r_mcbond_it2.012
r_mcbond_other2
r_angle_refined_deg1.57
r_angle_other_deg0.8
r_chiral_restr0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.068
r_dihedral_angle_3_deg11.765
r_dihedral_angle_4_deg8.066
r_dihedral_angle_1_deg7.553
r_mcangle_it2.674
r_mcbond_it2.012
r_mcbond_other2
r_angle_refined_deg1.57
r_angle_other_deg0.8
r_chiral_restr0.112
r_gen_planes_refined0.015
r_bond_refined_d0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1562
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms79

Software

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