8H1B

Crystal structure of MnmM from S. aureus complexed with SAM and tRNA anti-codon stem loop (ASL) (1.55 A)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAlphaFold model (UniProt: Q2FXG9)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 20% w/v PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.4750.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.436α = 90
b = 71.494β = 111.6
c = 67.267γ = 90
Symmetry
Space GroupP 1 21 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
11.5547.1284.60.0880.0950.0350.99811.87.265003
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)
11.551.6629.61.4211.5310.5660.5371.47.2

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 REPLACEMENTTHROUGHOUTAlphaFold model (UniProt: Q2FXG9)1.5547.1261827317584.550.17580.174320.20433RANDOM29.176
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]
-0.18-0.11-0.040.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.884
r_dihedral_angle_4_deg17.453
r_dihedral_angle_3_deg12.963
r_dihedral_angle_1_deg6.251
r_long_range_B_refined5.421
r_long_range_B_other5.25
r_scangle_other2.006
r_angle_refined_deg1.52
r_mcangle_it1.425
r_mcangle_other1.424
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.884
r_dihedral_angle_4_deg17.453
r_dihedral_angle_3_deg12.963
r_dihedral_angle_1_deg6.251
r_long_range_B_refined5.421
r_long_range_B_other5.25
r_scangle_other2.006
r_angle_refined_deg1.52
r_mcangle_it1.425
r_mcangle_other1.424
r_scbond_it1.295
r_scbond_other1.295
r_angle_other_deg1.235
r_mcbond_it0.907
r_mcbond_other0.905
r_chiral_restr0.098
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3028
Nucleic Acid Atoms710
Solvent Atoms421
Heterogen Atoms55

Software

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