Experiment: 4DO1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DNZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.1M Bis-Tris, 1.45M ammonium sulfate, 0.1M sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.72	66.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.021	α = 90
b = 143.479	β = 90
c = 172.768	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9796	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	50	100	0.098	0.112	28.5	7.1	179187	179187	1	1	23.581

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	100		0.319	0.297	5.23	6.1	8882

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4DNZ	2	43.67	170357	169438	8939	99.46	0.169	0.15545	0.15369	0.18886	RANDOM	23.518

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]
0.42			-1.37		0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.899
r_dihedral_angle_4_deg	18.022
r_dihedral_angle_3_deg	12.698
r_dihedral_angle_1_deg	6.015
r_scangle_it	5.911
r_scbond_it	3.831
r_mcangle_it	2.178
r_angle_refined_deg	2.091
r_mcbond_it	1.33
r_chiral_restr	0.185

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.899
r_dihedral_angle_4_deg	18.022
r_dihedral_angle_3_deg	12.698
r_dihedral_angle_1_deg	6.015
r_scangle_it	5.911
r_scbond_it	3.831
r_mcangle_it	2.178
r_angle_refined_deg	2.091
r_mcbond_it	1.33
r_chiral_restr	0.185
r_bond_refined_d	0.031
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12084
Nucleic Acid Atoms
Solvent Atoms	2197
Heterogen Atoms	269

Software

Software
Software Name	Purpose
HKL-2000	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	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.