Experiment: 7NIM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ACH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	295	3.5 M NaCl, 0.1 M citric acid pH 4.0. 20-25 mg/ml LsAA9A. 2 ul hanging drops (1:1 protein:reservoir ratio).

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.179	α = 90
b = 125.179	β = 90
c = 125.179	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 PILATUS 6M		2019-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.45	44.3	100	0.165	0.999	20.57	70.1		59727

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.54	99.8		1.846	0.71		41.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5ACH	1.45	44.3	56643	3009	99.98	0.1683	0.1672	0.17	0.1873	0.19	RANDOM	21.047

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_2_deg	29.535
r_dihedral_angle_4_deg	11.84
r_dihedral_angle_3_deg	8.61
r_dihedral_angle_1_deg	6.851
r_angle_refined_deg	2.083
r_angle_other_deg	1.584
r_chiral_restr	0.133
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.535
r_dihedral_angle_4_deg	11.84
r_dihedral_angle_3_deg	8.61
r_dihedral_angle_1_deg	6.851
r_angle_refined_deg	2.083
r_angle_other_deg	1.584
r_chiral_restr	0.133
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1788
Nucleic Acid Atoms
Solvent Atoms	395
Heterogen Atoms	148

Software

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

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.