6FBO

Human Methionine Adenosyltransferase II mutant (S114A) in I222 crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A1I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729830% PEG600 0.1M HEPES pH.7.0
Crystal Properties
Matthews coefficientSolvent content
2.1943.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.621α = 90
b = 94.682β = 90
c = 116.55γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.97DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.858.2899.90.170.2080.1190.9795.85.33450717.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.841000.7660.940.5380.7825.4

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 REPLACEMENTTHROUGHOUT5A1I1.858.2832796169799.810.152150.150980.17436RANDOM21.776
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]
3.48-0.87-2.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.13
r_dihedral_angle_4_deg19.655
r_dihedral_angle_3_deg13.112
r_dihedral_angle_1_deg6.413
r_long_range_B_refined5.664
r_long_range_B_other5.627
r_scangle_other3.824
r_angle_other_deg3.655
r_scbond_it2.437
r_scbond_other2.436
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.13
r_dihedral_angle_4_deg19.655
r_dihedral_angle_3_deg13.112
r_dihedral_angle_1_deg6.413
r_long_range_B_refined5.664
r_long_range_B_other5.627
r_scangle_other3.824
r_angle_other_deg3.655
r_scbond_it2.437
r_scbond_other2.436
r_mcangle_it2.293
r_mcangle_other2.293
r_angle_refined_deg1.671
r_mcbond_it1.524
r_mcbond_other1.522
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_gen_planes_other0.009
r_bond_other_d
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 Atoms2958
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing