Experiment: 8TR4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5V3Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	290	0.1 M TRIS-HCL, 2.0-1.8 M AMMONIUM SULFATE, 2%-5% V/V PPG P400

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.942	α = 90
b = 87.592	β = 90
c = 109.382	γ = 90

Symmetry
Space Group	P 2 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	PIXEL	DECTRIS PILATUS 6M		2020-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00003	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	48.37	92.1	0.088	0.052	0.997	10.1	3.3		30403

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	68		0.648	0.54	0.633	1.8	2.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	48.37	28866	1511	91.4	0.18711	0.18454	0.23764	RANDOM	37.196

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]
0.25			-0.39		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.033
r_dihedral_angle_1_deg	6.783
r_long_range_B_refined	6.725
r_long_range_B_other	6.68
r_scangle_other	3.933
r_mcangle_other	3.189
r_mcangle_it	3.188
r_scbond_it	2.846
r_scbond_other	2.546
r_mcbond_it	2.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.033
r_dihedral_angle_1_deg	6.783
r_long_range_B_refined	6.725
r_long_range_B_other	6.68
r_scangle_other	3.933
r_mcangle_other	3.189
r_mcangle_it	3.188
r_scbond_it	2.846
r_scbond_other	2.546
r_mcbond_it	2.06
r_mcbond_other	2.058
r_angle_refined_deg	1.092
r_angle_other_deg	0.4
r_chiral_restr	0.053
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4294
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	98

Software

Software
Software Name	Purpose
PDB-REDO	refinement
XDS	data reduction
Aimless	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.