Experiment: 7PN6

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	291	1.45M sodium potassium phosphate pH 5.6, 3% MPD Soaking: 10 mM myristic acid, 18 hours, cryoprotected with 25% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.205	α = 90
b = 57.908	β = 109.46
c = 61.121	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M	KB MIRRORS	2020-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979260	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.5	48.33	99.9	0.106	0.115	0.044	15.1	6.6		54034

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	100		0.642	0.699	0.274	5.6	6.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5OXU	1.5	48.33	51357	2658	99.89	0.1639	0.1627	0.1888	RANDOM	13.026

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]
-0.52		0.23	-0.65		0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.48
r_dihedral_angle_4_deg	17.145
r_dihedral_angle_3_deg	13.458
r_dihedral_angle_1_deg	5.688
r_angle_other_deg	1.579
r_angle_refined_deg	1.492
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.48
r_dihedral_angle_4_deg	17.145
r_dihedral_angle_3_deg	13.458
r_dihedral_angle_1_deg	5.688
r_angle_other_deg	1.579
r_angle_refined_deg	1.492
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.009
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2517
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	136

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	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.