Experiment: 7ZSF

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XB5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	100 mM sodium acetate pH 4.5, 10 % poly-ethylene glycol 20,000, 3 % glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.569	α = 90
b = 82.569	β = 90
c = 87.365	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 EIGER2 XE 16M		2019-07-04	M	SINGLE WAVELENGTH
2	1	x-ray	50	PIXEL	DECTRIS PILATUS 12M		2020-07-29	M	SINGLE WAVELENGTH
3	1	x-ray	50	PIXEL	DECTRIS PILATUS 12M		2020-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9796	Diamond	I03
2	SYNCHROTRON	DIAMOND BEAMLINE I23	4.42801	Diamond	I23
3	SYNCHROTRON	DIAMOND BEAMLINE I23	4.27532	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.36	87.29	99.97	0.075	0.079	0.025	17.1	19.9		74252

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	1.36	1.4	100		3.543	3.48	0.779	0.519	1.1	19.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4XB5	1.36	55.396	74207	3699	99.884	0.19	0.189	0.19	0.2179	0.22	RANDOM	25.954

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]
0.001			0.001		-0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.514
r_dihedral_angle_4_deg	16.814
r_dihedral_angle_3_deg	12.579
r_lrange_it	7.807
r_dihedral_angle_1_deg	5.822
r_scangle_it	4.593
r_scbond_it	3.173
r_mcangle_it	3.096
r_mcbond_it	2.152
r_angle_refined_deg	1.957

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.514
r_dihedral_angle_4_deg	16.814
r_dihedral_angle_3_deg	12.579
r_lrange_it	7.807
r_dihedral_angle_1_deg	5.822
r_scangle_it	4.593
r_scbond_it	3.173
r_mcangle_it	3.096
r_mcbond_it	2.152
r_angle_refined_deg	1.957
r_nbtor_refined	0.314
r_symmetry_nbd_refined	0.275
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.205
r_chiral_restr	0.117
r_bond_refined_d	0.012
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2376
Nucleic Acid Atoms
Solvent Atoms	388
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
MOLREP	phasing
SHELXCD	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.