7Y7U | pdb_00007y7u

Dimeric structure of a Quorum-Quenching metallo-hydrolase, LrsL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P9E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	1.6 M tri-Sodium citrate tribasic

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.51	α = 90
b = 166.51	β = 90
c = 166.51	γ = 90

Symmetry
Space Group	P 41 3 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		2022-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.987	SOLEIL	PROXIMA 1

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	1.89	46.18	99.97	0.1542	0.1552	0.01717	1	31.63	81.3		63574			44.72

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	1.89	1.958	99.98		6.561	6.601	0.7185	0.368	0.71	83.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1P9E	1.89	46.18	63574	2000	99.881	0.192	0.1908	0.19	0.2349	0.23	47.577

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.198
r_dihedral_angle_6_deg	16.01
r_lrange_it	10.418
r_scangle_it	8.044
r_dihedral_angle_1_deg	7.404
r_dihedral_angle_2_deg	7.349
r_scbond_it	5.816
r_mcangle_it	5.536
r_mcbond_it	4.208
r_angle_refined_deg	1.719
r_nbtor_refined	0.313
r_nbd_refined	0.211
r_symmetry_nbd_refined	0.198
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.137
r_chiral_restr	0.11
r_metal_ion_refined	0.048
r_bond_refined_d	0.011
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4386
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
BALBES	phasing