8H1A | pdb_00008h1a

Crystal structure of MnmM from S. aureus in apo state (1.44 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 sodium acetate trihydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.08

Crystal Data

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

Symmetry
Space Group	P 21 21 21

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)	0.97965	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	1.44	47.34	95.5	0.073	0.076	0.021	0.999	17.1	13.3		67371			20.9

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)	Redundancy	Number Unique Reflections (All)
1	1.44	1.54	66.5		1.955	2.025	0.525	0.605	1.5	14.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	AlphaFold model (UniProt: Q2FXG9)	1.44	47.34	63959	3409	84.1	0.15394	0.15185	0.16	0.19218	0.2	RANDOM	26.467

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			-0.29		1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.636
r_dihedral_angle_4_deg	15.031
r_dihedral_angle_3_deg	12.328
r_dihedral_angle_1_deg	6.467
r_long_range_B_refined	4.411
r_long_range_B_other	4.021
r_scangle_other	3.322
r_mcangle_it	2.835
r_mcangle_other	2.826
r_scbond_it	2.679
r_scbond_other	2.678
r_rigid_bond_restr	2.432
r_mcbond_it	2.094
r_mcbond_other	2.084
r_angle_refined_deg	1.482
r_angle_other_deg	1.235
r_chiral_restr	0.114
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2860
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms

Software

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