Experiment: 7WKZ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6A7P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	32% PEG 3350, 50mM potassium phosphate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.998	α = 90
b = 183.182	β = 106.514
c = 59.175	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 EIGER X 16M		2021-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

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	2.99	50	98.4	0.104	12.44	6.2		24010

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	2.99	3.1	95.2		1.114	1.52	5.5

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	6A7P	2.992	48.231	23776	1222	97.997	0.199	0.1961	0.2461	82.163

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]
19.331		5.167	19.059		-38.389

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.729
r_lrange_it	18.407
r_dihedral_angle_3_deg	15.029
r_mcangle_it	13.892
r_scangle_it	13.647
r_dihedral_angle_4_deg	13.461
r_scbond_it	9.897
r_mcbond_it	9.524
r_dihedral_angle_1_deg	4.833
r_angle_refined_deg	1.234

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.729
r_lrange_it	18.407
r_dihedral_angle_3_deg	15.029
r_mcangle_it	13.892
r_scangle_it	13.647
r_dihedral_angle_4_deg	13.461
r_scbond_it	9.897
r_mcbond_it	9.524
r_dihedral_angle_1_deg	4.833
r_angle_refined_deg	1.234
r_symmetry_nbd_refined	0.333
r_nbtor_refined	0.295
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.188
r_symmetry_xyhbond_nbd_refined	0.1
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8337
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	106

Software

Software
Software Name	Purpose
REFMAC	refinement
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.