9ERG | pdb_00009erg

Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with Mannose-1-Phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7285
Crystal Properties
Matthews coefficientSolvent content
2.3647.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.534α = 90
b = 83.368β = 106.352
c = 73.206γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2023-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979261ALBAXALOC

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
12.148.796.70.0857.13.440738
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.210.707

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.145.18440716207396.5220.1770.17540.18440.20930.211439.547
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]
0.772-1.070.126-0.231
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg13.086
r_dihedral_angle_3_deg11.526
r_dihedral_angle_1_deg7.257
r_lrange_it6.163
r_lrange_other6.128
r_dihedral_angle_2_deg5.197
r_scangle_it3.594
r_scangle_other3.594
r_mcangle_it2.509
r_mcangle_other2.509
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg13.086
r_dihedral_angle_3_deg11.526
r_dihedral_angle_1_deg7.257
r_lrange_it6.163
r_lrange_other6.128
r_dihedral_angle_2_deg5.197
r_scangle_it3.594
r_scangle_other3.594
r_mcangle_it2.509
r_mcangle_other2.509
r_scbond_it2.228
r_scbond_other2.228
r_mcbond_it1.647
r_mcbond_other1.647
r_angle_refined_deg1.312
r_angle_other_deg0.46
r_symmetry_nbd_refined0.211
r_nbd_other0.197
r_symmetry_nbd_other0.189
r_nbd_refined0.184
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.144
r_symmetry_xyhbond_nbd_refined0.144
r_symmetry_xyhbond_nbd_other0.111
r_symmetry_nbtor_other0.082
r_ncsr_local_group_10.077
r_chiral_restr0.061
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5441
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing