4MHO

Crystal structure of Gpb in complex with S3, SUGAR (N-[(BIPHENYL-4-YLOXY)ACETYL]-BETA-D-GLUCOPYRANOSYLAMINE)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SYMpdb entry 3SYM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.728910mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5952.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.91α = 90
b = 128.91β = 90
c = 116.89γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMAR CCD 165 mm2013-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.04027MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1223.9479.70.0737.625256652566-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1183.10.3472.71.97918

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 3SYM223.64996549965259078.580.16420.162370.19959RANDOM31.169
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]
0.750.75-1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.335
r_dihedral_angle_4_deg18.756
r_dihedral_angle_3_deg16.179
r_long_range_B_refined5.654
r_dihedral_angle_1_deg5.596
r_mcangle_it2.548
r_scbond_it2.245
r_mcbond_it1.596
r_angle_refined_deg1.25
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.335
r_dihedral_angle_4_deg18.756
r_dihedral_angle_3_deg16.179
r_long_range_B_refined5.654
r_dihedral_angle_1_deg5.596
r_mcangle_it2.548
r_scbond_it2.245
r_mcbond_it1.596
r_angle_refined_deg1.25
r_chiral_restr0.096
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms6577
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms28

Software

Software
Software NamePurpose
MAR345data collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing