4AD5

Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with glucose-1,3-deoxymannojirimycin and alpha-1,2-mannobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.1 M SODIUM ACETATE PH 4.9, 20% W/V PEG 2000 MME, 1.6% PGA-LM (POLY-GAMMA-GLUTAMIC ACID LOW MOLECULAR WEIGHT)
Crystal Properties
Matthews coefficientSolvent content
2.3347.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.844α = 90
b = 108.844β = 90
c = 67.762γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMARRESEARCHOSMICS MULTILAYER OPTICS2011-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
11.9401000.0619.56.131280225.6
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)
11.921000.237.16

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 STRUCTURE OF CLOSELY RELATED HOMOLOG1.939.5325505136085.730.160520.158130.2053RANDOM25.457
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]
0.380.38-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.193
r_dihedral_angle_4_deg15.077
r_dihedral_angle_3_deg14.848
r_dihedral_angle_1_deg5.996
r_angle_refined_deg1.207
r_mcangle_it1.207
r_nbtor_refined0.314
r_nbd_refined0.196
r_symmetry_vdw_refined0.152
r_symmetry_hbond_refined0.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.193
r_dihedral_angle_4_deg15.077
r_dihedral_angle_3_deg14.848
r_dihedral_angle_1_deg5.996
r_angle_refined_deg1.207
r_mcangle_it1.207
r_nbtor_refined0.314
r_nbd_refined0.196
r_symmetry_vdw_refined0.152
r_symmetry_hbond_refined0.147
r_xyhbond_nbd_refined0.142
r_chiral_restr0.088
r_bond_refined_d0.011
r_mcbond_it0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2819
Nucleic Acid Atoms
Solvent Atoms449
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing