6FBP

Human Methionine Adenosyltransferase II mutant (S114A) in P22121 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
Crystal Properties
Matthews coefficientSolvent content
2.0840.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.09α = 90
b = 102.871β = 90
c = 108.17γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9SOLEILPROXIMA 1

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
11.6554.0897.70.1080.1280.0680.99585.38170414.9
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)
11.651.6898.40.5660.6810.3720.6851.95.3

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 REPLACEMENTTHROUGHOUT5a1i1.6554.0877575409297.20.164670.163160.19456RANDOM19.747
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]
2.28-0.84-1.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.232
r_dihedral_angle_4_deg17.295
r_dihedral_angle_3_deg13.496
r_dihedral_angle_1_deg6.403
r_long_range_B_refined5.819
r_long_range_B_other5.819
r_scangle_other3.707
r_scbond_it2.393
r_scbond_other2.392
r_mcangle_it2.203
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.232
r_dihedral_angle_4_deg17.295
r_dihedral_angle_3_deg13.496
r_dihedral_angle_1_deg6.403
r_long_range_B_refined5.819
r_long_range_B_other5.819
r_scangle_other3.707
r_scbond_it2.393
r_scbond_other2.392
r_mcangle_it2.203
r_mcangle_other2.203
r_angle_refined_deg1.76
r_mcbond_it1.482
r_mcbond_other1.482
r_angle_other_deg1.034
r_chiral_restr0.11
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms5855
Nucleic Acid Atoms
Solvent Atoms488
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing