4D4B

The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with MSMSMe


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
2.2144.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.55α = 90
b = 85.226β = 90
c = 102.003γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-04-24MSINGLE 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
11.343.81000.0621.512.8178799-3.715.6
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)
11.31.3299.91.222.310.4

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 STRUCTURE1.365.4170002869599.990.122470.120970.15161RANDOM22.501
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]
0.03-0.090.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.601
r_sphericity_free36.348
r_dihedral_angle_4_deg25.646
r_sphericity_bonded12.137
r_dihedral_angle_3_deg11.548
r_dihedral_angle_1_deg5.679
r_scangle_it3.142
r_scbond_it2.761
r_rigid_bond_restr2.535
r_mcangle_it2.462
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.601
r_sphericity_free36.348
r_dihedral_angle_4_deg25.646
r_sphericity_bonded12.137
r_dihedral_angle_3_deg11.548
r_dihedral_angle_1_deg5.679
r_scangle_it3.142
r_scbond_it2.761
r_rigid_bond_restr2.535
r_mcangle_it2.462
r_mcbond_it2.048
r_mcbond_other2.048
r_angle_refined_deg1.386
r_angle_other_deg0.86
r_symmetry_vdw_refined0.358
r_symmetry_vdw_other0.321
r_nbd_refined0.269
r_symmetry_hbond_refined0.237
r_nbtor_refined0.19
r_nbd_other0.184
r_xyhbond_nbd_refined0.125
r_xyhbond_nbd_other0.118
r_chiral_restr0.088
r_nbtor_other0.081
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_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 Atoms5382
Nucleic Acid Atoms
Solvent Atoms1035
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing