4D4D

The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with 1,6-ManIFG


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
2.2745.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.94α = 90
b = 85.841β = 90
c = 103.256γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-05-22MSINGLE 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
11.444.299.50.0616.28.2146171-3.713
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)
11.41.4297.90.772.68.1

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 STRUCTURE1.466.01138951713299.470.114270.112860.14188RANDOM18.069
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]
-0.16-0.110.27
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free44.72
r_dihedral_angle_2_deg37.711
r_dihedral_angle_4_deg24.647
r_dihedral_angle_3_deg11.637
r_sphericity_bonded11.471
r_dihedral_angle_1_deg5.27
r_long_range_B_refined5.001
r_long_range_B_other3.82
r_scangle_other2.878
r_scbond_it2.479
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free44.72
r_dihedral_angle_2_deg37.711
r_dihedral_angle_4_deg24.647
r_dihedral_angle_3_deg11.637
r_sphericity_bonded11.471
r_dihedral_angle_1_deg5.27
r_long_range_B_refined5.001
r_long_range_B_other3.82
r_scangle_other2.878
r_scbond_it2.479
r_scbond_other2.473
r_rigid_bond_restr2.123
r_mcangle_it1.875
r_mcangle_other1.875
r_mcbond_it1.552
r_mcbond_other1.552
r_angle_refined_deg1.292
r_angle_other_deg0.863
r_chiral_restr0.087
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5400
Nucleic Acid Atoms
Solvent Atoms939
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing