6RK7

Inter-dimeric interface controls function and stability of S-methionine adenosyltransferase from U. urealiticum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6RJS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1M Hepes pH 7.0 and 30% Jeffamine ED-2001
Crystal Properties
Matthews coefficientSolvent content
2.7955.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.999α = 90
b = 106.139β = 96.86
c = 234.377γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

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
11.848.6699.80.0330.9969.44.7255563
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.830.5660.503

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 REPLACEMENTTHROUGHOUT6RJS1.848.662425801286399.780.170170.168860.19448RANDOM37.234
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]
-0.721.08-1.051.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.567
r_dihedral_angle_4_deg19.448
r_dihedral_angle_3_deg14.031
r_long_range_B_refined6.66
r_long_range_B_other6.629
r_dihedral_angle_1_deg6.266
r_scangle_other4.783
r_scbond_it3.149
r_scbond_other3.148
r_mcangle_it3.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.567
r_dihedral_angle_4_deg19.448
r_dihedral_angle_3_deg14.031
r_long_range_B_refined6.66
r_long_range_B_other6.629
r_dihedral_angle_1_deg6.266
r_scangle_other4.783
r_scbond_it3.149
r_scbond_other3.148
r_mcangle_it3.087
r_mcangle_other3.087
r_mcbond_it2.218
r_mcbond_other2.217
r_angle_refined_deg2.154
r_angle_other_deg1.122
r_chiral_restr0.154
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms17633
Nucleic Acid Atoms
Solvent Atoms1420
Heterogen Atoms330

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing