8OFO | pdb_00008ofo

Structure of Enterococcus faecium CdaA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.5 M Lithium sulfate 0.05 M TRIS pH 8.5 5 % (v/v) Glycerol 0.005 M Magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.16	α = 90
b = 99.16	β = 90
c = 112.18	γ = 120

Symmetry
Space Group	P 63 2 2

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 16M		2021-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976264	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.45	50	100	0.379	0.385	0.998	17.4	37		12518

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.51			3.429	3.4730000000000003	0.792

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.45	49.58	12516	626	99.952	0.209	0.2053	0.21	0.2743	0.27	55.996

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]
-0.246	-0.123		-0.246		0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.959
r_dihedral_angle_4_deg	18.273
r_dihedral_angle_3_deg	18.25
r_lrange_it	11.931
r_lrange_other	11.93
r_scangle_it	9.296
r_scangle_other	9.293
r_dihedral_angle_1_deg	7.907
r_mcangle_it	6.637
r_mcangle_other	6.634
r_scbond_it	6.405
r_scbond_other	6.402
r_mcbond_it	4.987
r_mcbond_other	4.987
r_angle_refined_deg	1.631
r_angle_other_deg	1.254
r_symmetry_nbd_refined	0.312
r_nbd_other	0.205
r_nbd_refined	0.193
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.164
r_nbtor_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.141
r_chiral_restr	0.077
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2285
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing