8H0S

Crystal structure of MnmM from B. subtilis complexed with Gln-TTG anti-codon stem loop and SAM (2.90 A)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dehydrate pH5.6, 30% w/v Polyethylene glycol 4,000, 3% w/v Trimethylamine N-oxide dihydrate
Crystal Properties
Matthews coefficientSolvent content
2.4349.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.18α = 90.97
b = 60.755β = 93.1
c = 94.059γ = 101.55
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2022-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)1.0000PAL/PLS5C (4A)

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
12.993.8891.20.1650.1950.1020.9926.63.518875
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)
12.93.0897.50.9951.1690.6070.7681.23.6

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 REPLACEMENTTHROUGHOUTPDB entry 4PON2.993.881793090190.980.242810.240760.2852RANDOM72.123
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]
4.780.847.38-8.951.663.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.538
r_long_range_B_refined13.789
r_long_range_B_other13.788
r_mcangle_it10.157
r_mcangle_other10.156
r_scangle_other9.356
r_dihedral_angle_2_deg8.287
r_dihedral_angle_1_deg7.61
r_mcbond_it6.268
r_mcbond_other6.265
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.538
r_long_range_B_refined13.789
r_long_range_B_other13.788
r_mcangle_it10.157
r_mcangle_other10.156
r_scangle_other9.356
r_dihedral_angle_2_deg8.287
r_dihedral_angle_1_deg7.61
r_mcbond_it6.268
r_mcbond_other6.265
r_scbond_it5.763
r_scbond_other5.76
r_angle_refined_deg1.263
r_angle_other_deg0.407
r_chiral_restr0.056
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms5423
Nucleic Acid Atoms710
Solvent Atoms110
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
MxDCdata collection
PDB_EXTRACTdata extraction
Cootmodel building