5A7V

The GH130 family of mannoside phosphorylases contains glycoside hydrolases that target beta-1,2 mannosidic linkages in Candida mannan


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QC2PDB ENTRY 3QC2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12.2 M AMMONIUM SULFATE
Crystal Properties
Matthews coefficientSolvent content
3.463

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.767α = 90
b = 118.11β = 90
c = 126.586γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
11.3546.5898.30.0510.73.42438801.810.3
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)
11.351.3798.80.531.83.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3QC21.35118.112437871201698.1930.1310.130.1497RANDOM16.99
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]
0.802-0.507-0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.284
r_dihedral_angle_2_deg29.07
r_dihedral_angle_4_deg14.452
r_sphericity_bonded12.198
r_dihedral_angle_3_deg11.603
r_dihedral_angle_1_deg7.397
r_scangle_it3.045
r_rigid_bond_restr2.83
r_scbond_it2.647
r_mcangle_it2.253
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.284
r_dihedral_angle_2_deg29.07
r_dihedral_angle_4_deg14.452
r_sphericity_bonded12.198
r_dihedral_angle_3_deg11.603
r_dihedral_angle_1_deg7.397
r_scangle_it3.045
r_rigid_bond_restr2.83
r_scbond_it2.647
r_mcangle_it2.253
r_mcbond_it1.75
r_mcbond_other1.731
r_angle_refined_deg1.707
r_angle_other_deg1.028
r_nbd_refined0.246
r_chiral_restr0.209
r_nbd_other0.206
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.11
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbtor_other
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5767
Nucleic Acid Atoms
Solvent Atoms857
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing