Experiment: 9DGD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6P3O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.75	293	26% pentaerythritol ethoxylate, 15 mM ammonium sulfate, 0.1M Tris-Cl, 0.5 mM boldine, 0.5 mM SAM, 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.02	α = 90
b = 104.02	β = 90
c = 82.597	γ = 120

Symmetry
Space Group	P 32 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 PILATUS 6M		2020-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9795	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	39.544	99.91	0.016	1	14.84	12.9		48088

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	100		0.437	0.697	1.14	11.5

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	39.544	48088	2460	99.917	0.169	0.1681	0.1688	0.1869	0.1872	RANDOM	36.251

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]
0.114	0.057		0.114		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.665
r_dihedral_angle_6_deg	12.321
r_lrange_it	11.19
r_scangle_it	9.544
r_scbond_it	7.139
r_dihedral_angle_1_deg	5.959
r_mcangle_it	5.582
r_dihedral_angle_2_deg	5.153
r_mcbond_it	4.742
r_angle_refined_deg	1.416

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.665
r_dihedral_angle_6_deg	12.321
r_lrange_it	11.19
r_scangle_it	9.544
r_scbond_it	7.139
r_dihedral_angle_1_deg	5.959
r_mcangle_it	5.582
r_dihedral_angle_2_deg	5.153
r_mcbond_it	4.742
r_angle_refined_deg	1.416
r_nbtor_refined	0.307
r_symmetry_xyhbond_nbd_refined	0.229
r_nbd_refined	0.221
r_symmetry_nbd_refined	0.195
r_xyhbond_nbd_refined	0.189
r_chiral_restr	0.092
r_gen_planes_refined	0.006
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2697
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	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.