4MI9

Crystal structure of Gpb in complex with SUGAR (N-[(3R)-3-(4-ETHYLPHENYL)BUTANOYL]-BETA-D-GLUCOPYRANOSYLAMINE) (S20)


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
2.5852.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.81α = 90
b = 128.81β = 90
c = 116.72γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMAR CCD 165 mm2013-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.04MAX 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
11.8523.8298.50.05610.22.68232582325-3
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)
11.851.9598.80.4142.32.511899

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 3SYM1.8523.587815978159411198.050.162910.16150.19018RANDOM32.917
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]
0.730.73-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.635
r_dihedral_angle_4_deg19.959
r_dihedral_angle_3_deg15.002
r_long_range_B_refined5.968
r_long_range_B_other5.967
r_dihedral_angle_1_deg5.844
r_scangle_other4.291
r_mcangle_it2.824
r_mcangle_other2.824
r_scbond_it2.605
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.635
r_dihedral_angle_4_deg19.959
r_dihedral_angle_3_deg15.002
r_long_range_B_refined5.968
r_long_range_B_other5.967
r_dihedral_angle_1_deg5.844
r_scangle_other4.291
r_mcangle_it2.824
r_mcangle_other2.824
r_scbond_it2.605
r_scbond_other2.605
r_mcbond_it1.821
r_mcbond_other1.82
r_angle_refined_deg1.279
r_angle_other_deg0.814
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6597
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms25

Software

Software
Software NamePurpose
MAR345data collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing