4U6D

Zg3615, a family 117 glycoside hydrolase in complex with beta-3,6-anhydro-L-galactose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4U6B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291The optimized condition for Zg3615 was: 0.1 M sodium acetate pH 5.0, 25% PEG 3350, in a 1:1 ratio of protein (at 10 mg/mL) to mother liquor.
Crystal Properties
Matthews coefficientSolvent content
2.2846.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.109α = 90
b = 226.132β = 90
c = 67.124γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.979SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.730100257.496642
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4U6B1.73091803483899.960.186550.184850.180.218880.22RANDOM22.37
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]
1.47-0.15-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.243
r_dihedral_angle_4_deg22.281
r_dihedral_angle_3_deg13.312
r_dihedral_angle_1_deg7.084
r_long_range_B_refined4.88
r_mcangle_it2.119
r_scbond_it1.972
r_angle_refined_deg1.571
r_mcbond_it1.466
r_chiral_restr0.112
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6160
Nucleic Acid Atoms
Solvent Atoms708
Heterogen Atoms110

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing