8H26

Crystal structure of MnmM from S. aureus complexed with SAH (1.50 A)

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.329	α = 91.25
b = 69.362	β = 112.97
c = 74.608	γ = 114.05

Symmetry
Space Group	P 1

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	1.5	67.09	92.7	0.069	0.074	0.028	0.999	14.7	7.3		104221			21.6

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	1.5	1.68	72.3		1.285	1.382	0.507	0.637	1.7	7.4

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)	1.5	67.09	98695	5112	63.35	0.18451	0.18281	0.21855	RANDOM	30.373

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]
0.06	0.04	0.02	0.51	0.01	-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.242
r_dihedral_angle_4_deg	16.372
r_dihedral_angle_3_deg	12.909
r_long_range_B_refined	7.05
r_long_range_B_other	7.013
r_dihedral_angle_1_deg	6.641
r_scangle_other	4.481
r_mcangle_other	3.15
r_mcangle_it	3.149
r_scbond_it	2.942
r_scbond_other	2.942
r_mcbond_it	2.132
r_mcbond_other	2.13
r_angle_refined_deg	1.652
r_angle_other_deg	1.207
r_chiral_restr	0.118
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8298
Nucleic Acid Atoms
Solvent Atoms	678
Heterogen Atoms	104

Software

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