Experiment: 8CRJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other	8CRI	Crystal structure of LplA1 in complex with lipoic acid (Listeria monocytogenes)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.1 M MES, 1.0 M LiCl, 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
4.61	73.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.31	α = 90
b = 79.31	β = 90
c = 225.14	γ = 90

Symmetry
Space Group	P 41 21 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		2022-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.6	30	98.4	0.053	15.4	4.5		22722

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.7			0.691	2.4	4.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	8CRI	2.6	30	21558	1135	98.6	0.1747	0.173	0.2061	RANDOM	74.053

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]
-0.79			-0.79		1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.226
r_dihedral_angle_4_deg	14.685
r_dihedral_angle_3_deg	13.146
r_dihedral_angle_1_deg	6.486
r_angle_refined_deg	1.166
r_angle_other_deg	1.042
r_rigid_bond_restr	0.529
r_chiral_restr	0.04
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.226
r_dihedral_angle_4_deg	14.685
r_dihedral_angle_3_deg	13.146
r_dihedral_angle_1_deg	6.486
r_angle_refined_deg	1.166
r_angle_other_deg	1.042
r_rigid_bond_restr	0.529
r_chiral_restr	0.04
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2710
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	116

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.