Experiment: 9W7O

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DY6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M lithium chloride, PEG 4000 20%

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.817	α = 90
b = 51.512	β = 113.075
c = 74.697	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	RIGAKU HyPix-6000HE		2024-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

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	1.8	24.887	99.9	0.961	11.8	6.1		46191

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	1.8	1.84			0.717

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.93	24.887	37522	1855	99.88	0.187	0.1842	0.1845	0.2384	0.2391	14.01

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]
0.659		-0.373	0.405		-0.548

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.447
r_dihedral_angle_3_deg	16.124
r_dihedral_angle_6_deg	14.968
r_dihedral_angle_1_deg	6.642
r_lrange_it	4.862
r_scangle_it	3.399
r_scbond_it	2.178
r_angle_refined_deg	1.948
r_mcangle_it	1.764
r_mcbond_it	1.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.447
r_dihedral_angle_3_deg	16.124
r_dihedral_angle_6_deg	14.968
r_dihedral_angle_1_deg	6.642
r_lrange_it	4.862
r_scangle_it	3.399
r_scbond_it	2.178
r_angle_refined_deg	1.948
r_mcangle_it	1.764
r_mcbond_it	1.098
r_nbtor_refined	0.31
r_symmetry_xyhbond_nbd_refined	0.24
r_symmetry_nbd_refined	0.234
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.183
r_chiral_restr	0.132
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4120
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms	82

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	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.