4D4C

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


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
2.1542.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.248α = 90
b = 85.285β = 90
c = 100.613γ = 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
11.343.399.80.0616.68173270-3.712.6
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)
11.31.3299.60.922.28

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 STRUCTURE1.365.06164705846699.690.176970.17530.20949RANDOM
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]
0.5-0.37-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.033
r_dihedral_angle_4_deg24.927
r_sphericity_free23.542
r_dihedral_angle_3_deg11.807
r_sphericity_bonded8.588
r_dihedral_angle_1_deg5.399
r_long_range_B_refined3.106
r_rigid_bond_restr2.948
r_long_range_B_other2.861
r_scangle_other2.696
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.033
r_dihedral_angle_4_deg24.927
r_sphericity_free23.542
r_dihedral_angle_3_deg11.807
r_sphericity_bonded8.588
r_dihedral_angle_1_deg5.399
r_long_range_B_refined3.106
r_rigid_bond_restr2.948
r_long_range_B_other2.861
r_scangle_other2.696
r_scbond_it2.45
r_scbond_other2.45
r_mcangle_it2.022
r_mcangle_other2.022
r_mcbond_it1.813
r_mcbond_other1.803
r_angle_refined_deg1.326
r_angle_other_deg0.817
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.007
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 Atoms5353
Nucleic Acid Atoms
Solvent Atoms709
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing