Experiment: 8BDS

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NW1	5nw1, 3mxf
experimental model	PDB	3MXF	5nw1, 3mxf

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	1.4M Ammonium Sulfate, 4% (w/v) glycerol, 0.1M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.031	α = 90
b = 79.031	β = 90
c = 204.206	γ = 120

Symmetry
Space Group	P 31 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		2022-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.718	68.443	95.9	0.076	0.081	0.026	0.999	15.2	9.4		63052

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.718	1.871	69.1		1.399	1.481	0.483	0.621		9.3

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	MOLECULAR REPLACEMENT	THROUGHOUT	5nw1, 3mxf	1.72	68.44	59918	3134	79.12	0.1692	0.1677	0.1973	RANDOM	37.641

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]
-0.04	-0.02		-0.04		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.514
r_dihedral_angle_4_deg	22.487
r_dihedral_angle_3_deg	13.121
r_dihedral_angle_1_deg	6.827
r_angle_refined_deg	1.824
r_angle_other_deg	1.463
r_chiral_restr	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.514
r_dihedral_angle_4_deg	22.487
r_dihedral_angle_3_deg	13.121
r_dihedral_angle_1_deg	6.827
r_angle_refined_deg	1.824
r_angle_other_deg	1.463
r_chiral_restr	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3763
Nucleic Acid Atoms
Solvent Atoms	396
Heterogen Atoms	115

Software

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