Experiment: 8WZO

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5N2W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, 7.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.976	α = 90
b = 47.747	β = 105.38
c = 127.859	γ = 90

Symmetry
Space Group	I 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 EIGER X 9M		2023-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.8731	ESRF	ID30B

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	2.25	44.52	99.8	0.993	8.4	4.3		21772

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	2.25	2.32			0.643

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5N2W	2.25	40.947	21769	1097	99.689	0.209	0.2072	0.2485	45.106

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]
-0.35		-1.342	-0.216		1.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.26
r_dihedral_angle_4_deg	17.773
r_dihedral_angle_3_deg	16.868
r_lrange_it	6.373
r_dihedral_angle_1_deg	5.645
r_scangle_it	2.89
r_mcangle_it	2.858
r_scbond_it	1.774
r_mcbond_it	1.616
r_angle_refined_deg	1.026

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.26
r_dihedral_angle_4_deg	17.773
r_dihedral_angle_3_deg	16.868
r_lrange_it	6.373
r_dihedral_angle_1_deg	5.645
r_scangle_it	2.89
r_mcangle_it	2.858
r_scbond_it	1.774
r_mcbond_it	1.616
r_angle_refined_deg	1.026
r_nbtor_refined	0.299
r_nbd_refined	0.184
r_symmetry_nbd_refined	0.179
r_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_refined	0.121
r_chiral_restr	0.078
r_bond_refined_d	0.004
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2929
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	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.