8H27

Crystal structure of MnmM from S. aureus complexed with SAM (2.04 A)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AlphaFold model (UniProt: Q2FXG9)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, and 25% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.015	α = 90
b = 114.015	β = 90
c = 67.009	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2022-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97949	PAL/PLS	5C (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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.04	43.46	84.6	0.108	0.112	0.03	0.999	17.8	13.9		46406			40.76

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)	Redundancy	Number Unique Reflections (All)
1	2.04	2.23	36.4		2.271	2.353	0.615	0.627	1.4	14.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	AlphaFold model (UniProt: Q2FXG9)	2.04	43.46	44157	2248	84.57	0.19058	0.18887	0.22359	RANDOM	53.712

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]
-0.21			-0.21		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.711
r_dihedral_angle_4_deg	14.911
r_dihedral_angle_3_deg	14.357
r_long_range_B_refined	7.055
r_long_range_B_other	7.001
r_dihedral_angle_1_deg	6.189
r_scangle_other	4.772
r_mcangle_it	3.971
r_mcangle_other	3.971
r_scbond_it	3.181
r_scbond_other	3.181
r_mcbond_it	2.676
r_mcbond_other	2.675
r_angle_refined_deg	1.313
r_angle_other_deg	1.068
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5635
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
MxDC	data collection
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing
Coot	model building
PDB_EXTRACT	data extraction