4AYQ

Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with mannoimidazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPREVIOUSLY SOLVED NATIVE STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.2 M AMMONIUM ACTETATE, 0.1 M BIS-TRIS PH 6.5, 22% WT/VOL PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9737.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.607α = 90
b = 143.607β = 90
c = 50.026γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2012-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.146.4199.20.0718.76.21549062
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)
11.11.1694.20.285.44.9

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 REPLACEMENTTHROUGHOUTPREVIOUSLY SOLVED NATIVE STRUCTURE1.141.49147134777299.140.089320.088480.10524RANDOM8.403
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.456
r_dihedral_angle_2_deg33.889
r_dihedral_angle_4_deg16.49
r_dihedral_angle_3_deg11.615
r_sphericity_bonded7.281
r_dihedral_angle_1_deg6.123
r_rigid_bond_restr1.614
r_angle_refined_deg1.392
r_angle_other_deg0.818
r_symmetry_vdw_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.456
r_dihedral_angle_2_deg33.889
r_dihedral_angle_4_deg16.49
r_dihedral_angle_3_deg11.615
r_sphericity_bonded7.281
r_dihedral_angle_1_deg6.123
r_rigid_bond_restr1.614
r_angle_refined_deg1.392
r_angle_other_deg0.818
r_symmetry_vdw_refined0.306
r_nbd_refined0.273
r_symmetry_vdw_other0.266
r_nbtor_refined0.193
r_nbd_other0.175
r_symmetry_hbond_refined0.158
r_xyhbond_nbd_refined0.106
r_xyhbond_nbd_other0.1
r_chiral_restr0.093
r_nbtor_other0.086
r_metal_ion_refined0.07
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3451
Nucleic Acid Atoms
Solvent Atoms827
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing