5GGD

Crystal structure of Mycobacterium smegmatis MutT1 in complex with phosphate and magnesium ions (excess magnesium, II)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FJY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH8.52930.2 M magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride, 30% w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
1.9938.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.95α = 90
b = 87.6β = 100.06
c = 90.53γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.95372ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.744.5799.96.63.265728
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.791001.53.1

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 REPLACEMENTTHROUGHOUT3FJY1.744.5762029331399.380.218340.216140.25863RANDOM31.036
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]
-1.492.31-3.213.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.339
r_dihedral_angle_4_deg16.982
r_dihedral_angle_3_deg15.019
r_dihedral_angle_1_deg6.793
r_long_range_B_refined6.73
r_long_range_B_other6.604
r_scangle_other4.906
r_mcangle_it3.636
r_mcangle_other3.636
r_scbond_it3.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.339
r_dihedral_angle_4_deg16.982
r_dihedral_angle_3_deg15.019
r_dihedral_angle_1_deg6.793
r_long_range_B_refined6.73
r_long_range_B_other6.604
r_scangle_other4.906
r_mcangle_it3.636
r_mcangle_other3.636
r_scbond_it3.315
r_scbond_other3.303
r_mcbond_it2.681
r_mcbond_other2.674
r_angle_refined_deg1.909
r_angle_other_deg0.874
r_chiral_restr0.111
r_bond_refined_d0.017
r_gen_planes_refined0.01
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 Atoms4556
Nucleic Acid Atoms
Solvent Atoms511
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing