8H0T | pdb_00008h0t

Crystal structure of MnmM from B. subtilis complexed with SAH (1.17 A)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PON	PDB entry 4PON

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M HEPES pH 7.5, 25% w/v PEG 3,350

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.555	α = 90
b = 55.387	β = 103.16
c = 60.592	γ = 90

Symmetry
Space Group	C 1 2 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		2021-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97926	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	1.16	37.59	72.5	0.098	0.106	0.041	0.999	11.6	6.5		41988

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	1.16	1.3			0.807	0.951	0.493	0.626	1.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4PON	1.17	37.59	39938	2049	74.46	0.13642	0.13489	0.14	0.16663	0.17	RANDOM	14.069

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]
-0.71		1.31	-1.34		1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.46
r_dihedral_angle_2_deg	8.867
r_dihedral_angle_1_deg	7.087
r_rigid_bond_restr	6.641
r_long_range_B_refined	5.451
r_long_range_B_other	5.449
r_scangle_other	4.755
r_scbond_it	3.939
r_scbond_other	3.939
r_mcangle_it	2.877
r_mcangle_other	2.876
r_mcbond_it	2.298
r_mcbond_other	2.292
r_angle_refined_deg	1.712
r_angle_other_deg	0.595
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_bond_other_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.005
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1416
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	26

Software

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