5GLX

Crystal structure of a glycoside hydrolase 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
1.6324.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.283α = 90
b = 58.868β = 115.01
c = 38.38γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

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
11.422599.40.06822.15.227662
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)
11.421.4799.10.1810.9744.9

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 REPLACEMENTTHROUGHOUT1OA71.422526261138099.290.13460.13320.1608RANDOM16.655
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]
-0.010.02-0.190.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.867
r_dihedral_angle_3_deg13.218
r_dihedral_angle_4_deg9.736
r_dihedral_angle_1_deg6.974
r_mcangle_it2.644
r_mcbond_it1.789
r_mcbond_other1.773
r_angle_refined_deg1.438
r_angle_other_deg0.792
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.867
r_dihedral_angle_3_deg13.218
r_dihedral_angle_4_deg9.736
r_dihedral_angle_1_deg6.974
r_mcangle_it2.644
r_mcbond_it1.789
r_mcbond_other1.773
r_angle_refined_deg1.438
r_angle_other_deg0.792
r_chiral_restr0.107
r_gen_planes_refined0.014
r_bond_refined_d0.012
r_gen_planes_other0.002
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1593
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms

Software

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