8H1A

Crystal structure of MnmM from S. aureus in apo state (1.44 A)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.6854.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.494α = 90
b = 63.91β = 90
c = 135.044γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2022-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.97965PAL/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
11.4447.3495.50.0730.0760.0210.99917.113.36737120.9
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)
11.441.5466.51.9552.0250.5250.6051.514.8

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)1.4447.3463959340984.10.153940.151850.19218RANDOM26.467
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]
-1.05-0.291.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.636
r_dihedral_angle_4_deg15.031
r_dihedral_angle_3_deg12.328
r_dihedral_angle_1_deg6.467
r_long_range_B_refined4.411
r_long_range_B_other4.021
r_scangle_other3.322
r_mcangle_it2.835
r_mcangle_other2.826
r_scbond_it2.679
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.636
r_dihedral_angle_4_deg15.031
r_dihedral_angle_3_deg12.328
r_dihedral_angle_1_deg6.467
r_long_range_B_refined4.411
r_long_range_B_other4.021
r_scangle_other3.322
r_mcangle_it2.835
r_mcangle_other2.826
r_scbond_it2.679
r_scbond_other2.678
r_rigid_bond_restr2.432
r_mcbond_it2.094
r_mcbond_other2.084
r_angle_refined_deg1.482
r_angle_other_deg1.235
r_chiral_restr0.114
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2860
Nucleic Acid Atoms
Solvent Atoms307
Heterogen Atoms

Software

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