9I25 | pdb_00009i25

WxLIP from Enterococcus faecium locus A bound to long WxL

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	7	300	sodium HEPES, PEG12000

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.147	α = 90
b = 105.147	β = 90
c = 67.172	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	300	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	1.91	54	100	0.251	0.257	0.056	0.998	8.1	21.1		32902

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	1.91	5.18	100		5.74	5.878	1.259	0.332	0.3	21.7

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	1.911	54	32871	1687	99.945	0.219	0.2172	0.2146	0.2609	0.2578	46.435

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]
0.082	0.041		0.082		-0.265

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.252
r_dihedral_angle_3_deg	17.067
r_dihedral_angle_2_deg	11.734
r_lrange_other	9.407
r_lrange_it	9.397
r_dihedral_angle_1_deg	9.276
r_scangle_it	6.961
r_scangle_other	6.959
r_mcangle_it	5.472
r_mcangle_other	5.47
r_scbond_it	4.72
r_scbond_other	4.718
r_mcbond_it	3.772
r_mcbond_other	3.769
r_angle_refined_deg	2.312
r_angle_other_deg	0.762
r_symmetry_xyhbond_nbd_refined	0.232
r_xyhbond_nbd_refined	0.229
r_symmetry_nbd_other	0.211
r_nbd_refined	0.209
r_nbd_other	0.207
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.148
r_chiral_restr	0.113
r_symmetry_nbtor_other	0.1
r_symmetry_xyhbond_nbd_other	0.07
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2068
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms

Software

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