6EXA | pdb_00006exa

Crystal structure of DotM cytoplasmic domain (residues 153-380), double mutant R196E/R197E

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EXB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.2 M lithium sulphate 0.1 M MES pH 6.0 20% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.466	α = 90
b = 118.466	β = 90
c = 66.471	γ = 120

Symmetry
Space Group	P 65

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 PILATUS 6M-F		2016-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.79	66.47	100	0.168	12	6.6		50188

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.82	100		0.046	0.672	2.6	6.5

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	6EXB	1.79	66.47	47264	2452	99.13	0.20508	0.20254	0.21	0.2538	0.26	RANDOM	35.269

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]
1.15	0.57		1.15		-3.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.645
r_dihedral_angle_4_deg	16.684
r_dihedral_angle_3_deg	15.098
r_long_range_B_refined	10.709
r_long_range_B_other	10.422
r_scangle_other	6.246
r_dihedral_angle_1_deg	6.064
r_mcangle_it	4.558
r_mcangle_other	4.557
r_scbond_it	4.367
r_scbond_other	4.091
r_mcbond_it	3.16
r_mcbond_other	3.16
r_angle_refined_deg	1.955
r_angle_other_deg	1.138
r_chiral_restr	0.12
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3530
Nucleic Acid Atoms
Solvent Atoms	345
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing