9I1Y | pdb_00009i1y

WxLIP from Enterococcus faecium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	300	lithium sulfate, sodium acetate, PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.54	α = 90
b = 102.719	β = 90
c = 118.795	γ = 90

Symmetry
Space Group	C 2 2 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 EIGER2 XE 16M		2023-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97622	Diamond	I03

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	1.95	51.4	99.9	0.116	0.12	0.032	0.999	12.7	13.7		45950

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	1.95	5.29	100		3.623	3.759	0.994	0.255	0.4

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	THROUGHOUT	1.95	51.4	45919	2050	99.765	0.194	0.1916	0.189	0.2466	0.2462	50.189

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]
0.427			-1.274		0.847

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.872
r_dihedral_angle_6_deg	17.546
r_dihedral_angle_2_deg	15.961
r_lrange_other	11.111
r_lrange_it	11.097
r_scangle_it	9.167
r_scangle_other	9.165
r_dihedral_angle_1_deg	7.992
r_scbond_it	6.714
r_scbond_other	6.714
r_mcangle_other	6.233
r_mcangle_it	6.227
r_mcbond_it	4.688
r_mcbond_other	4.687
r_angle_refined_deg	2.175
r_angle_other_deg	0.694
r_symmetry_nbd_refined	0.261
r_symmetry_xyhbond_nbd_refined	0.24
r_xyhbond_nbd_refined	0.221
r_nbd_refined	0.214
r_symmetry_nbd_other	0.213
r_nbtor_refined	0.188
r_nbd_other	0.178
r_symmetry_nbtor_other	0.098
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4175
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	37

Software

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