6JT8

Crystal structure of 450-451_deletion mutant of FGAM Synthetase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T3T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2982M Ammonium Sulphate
Crystal Properties
Matthews coefficientSolvent content
3.160.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 147.151α = 90
b = 147.151β = 90
c = 141.346γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2018-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.9501000.03527.069.3136288
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.930.172

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 REPLACEMENTTHROUGHOUT1T3T1.948.17129371685699.810.127090.125420.15864RANDOM19.637
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.417
r_dihedral_angle_4_deg18.211
r_dihedral_angle_3_deg14.125
r_long_range_B_refined7.575
r_long_range_B_other7.276
r_dihedral_angle_1_deg6.583
r_scangle_other4.77
r_scbond_it3.328
r_scbond_other3.325
r_mcangle_it2.461
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.417
r_dihedral_angle_4_deg18.211
r_dihedral_angle_3_deg14.125
r_long_range_B_refined7.575
r_long_range_B_other7.276
r_dihedral_angle_1_deg6.583
r_scangle_other4.77
r_scbond_it3.328
r_scbond_other3.325
r_mcangle_it2.461
r_mcangle_other2.461
r_angle_refined_deg2.097
r_mcbond_it1.868
r_mcbond_other1.865
r_angle_other_deg1.117
r_chiral_restr0.131
r_bond_refined_d0.022
r_gen_planes_refined0.011
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 Atoms9913
Nucleic Acid Atoms
Solvent Atoms1358
Heterogen Atoms267

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing