5MI6

BtGH84 mutant with covalent modification by MA3 in complex with Thiamet G


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CHO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82984% PEG 8K, 125mM Imidazole, 3% TMAO, 15% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
3.1260.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 196.023α = 90
b = 51.662β = 113.34
c = 112.258γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
1249.6699.50.1120.994.43.170077
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)
122.1699.50.751.23

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 REPLACEMENTTHROUGHOUT2CHO249.6666476351799.540.201190.199160.24007RANDOM36.712
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]
1.78-3.37-0.681.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.114
r_dihedral_angle_3_deg15.512
r_dihedral_angle_4_deg15.072
r_long_range_B_refined6.648
r_long_range_B_other6.546
r_dihedral_angle_1_deg6.503
r_scangle_other4.572
r_mcangle_it3.654
r_mcangle_other3.653
r_scbond_it2.869
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.114
r_dihedral_angle_3_deg15.512
r_dihedral_angle_4_deg15.072
r_long_range_B_refined6.648
r_long_range_B_other6.546
r_dihedral_angle_1_deg6.503
r_scangle_other4.572
r_mcangle_it3.654
r_mcangle_other3.653
r_scbond_it2.869
r_scbond_other2.869
r_mcbond_it2.328
r_mcbond_other2.327
r_angle_refined_deg1.567
r_angle_other_deg0.958
r_chiral_restr0.091
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5569
Nucleic Acid Atoms
Solvent Atoms325
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing