Experiment: 9EWM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7LKU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG 3350, 0.1 mM benzamidine hydrochloride, 200 mM potassium formate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.136	α = 90
b = 53.802	β = 100.174
c = 45.286	γ = 90

Symmetry
Space Group	C 1 2 1

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 PILATUS3 S 6M		2023-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9677	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.63	57.65	83.1	0.989	6.3	6.5		12088

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.63	2.85			0.322

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.63	48.802	7174	346	85.476	0.244	0.2392	0.336	44.221

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]
-0.527		-0.398	-0.611		1.203

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.413
r_lrange_it	19.303
r_scangle_it	17.238
r_dihedral_angle_6_deg	15.143
r_dihedral_angle_3_deg	14.999
r_mcangle_it	14.441
r_scbond_it	13.206
r_mcbond_it	10.645
r_dihedral_angle_1_deg	7.803
r_angle_refined_deg	1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.413
r_lrange_it	19.303
r_scangle_it	17.238
r_dihedral_angle_6_deg	15.143
r_dihedral_angle_3_deg	14.999
r_mcangle_it	14.441
r_scbond_it	13.206
r_mcbond_it	10.645
r_dihedral_angle_1_deg	7.803
r_angle_refined_deg	1.6
r_nbtor_refined	0.32
r_nbd_refined	0.25
r_xyhbond_nbd_refined	0.21
r_symmetry_nbd_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.074
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2320
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	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.