5AGD

An inactive (D125N) variant of the catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with alpha-1,6-mannopentaose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 M AMMONIUM NITRATE, PH 6.5, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2445.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.52α = 90
b = 85.725β = 90
c = 102.613γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.244.0299.50.0418.67.9228606-3.7
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)
11.21.2294.211.97.7

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 APO STRUCTURE1.265.792173691113699.420.121690.120540.14417RANDOM22.036
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]
0.28-0.340.06
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.895
r_dihedral_angle_2_deg38.487
r_dihedral_angle_4_deg24.324
r_sphericity_bonded13.026
r_dihedral_angle_3_deg11.031
r_dihedral_angle_1_deg5.292
r_rigid_bond_restr2.754
r_scangle_it2.622
r_scbond_it2.264
r_mcangle_it2.005
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.895
r_dihedral_angle_2_deg38.487
r_dihedral_angle_4_deg24.324
r_sphericity_bonded13.026
r_dihedral_angle_3_deg11.031
r_dihedral_angle_1_deg5.292
r_rigid_bond_restr2.754
r_scangle_it2.622
r_scbond_it2.264
r_mcangle_it2.005
r_mcbond_it1.719
r_mcbond_other1.716
r_angle_refined_deg1.436
r_angle_other_deg1.147
r_symmetry_hbond_refined0.465
r_symmetry_hbond_other0.283
r_symmetry_vdw_refined0.281
r_symmetry_vdw_other0.265
r_nbd_refined0.261
r_nbtor_refined0.19
r_nbd_other0.187
r_xyhbond_nbd_refined0.13
r_chiral_restr0.104
r_nbtor_other0.075
r_xyhbond_nbd_other0.049
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_metal_ion_refined
r_metal_ion_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 Atoms5372
Nucleic Acid Atoms
Solvent Atoms1032
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing