Experiment: 7TH5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3APY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	297	0.1M Tris-HCl pH 8.5, 3M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.496	α = 90
b = 91.288	β = 90
c = 130.261	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	PIXEL	DECTRIS PILATUS3 6M		2018-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

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	2.09	47.07	98.7	0.118	0.138	0.069	0.993	7.6	3.9		42742

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	2.09	2.15	88.4		0.621	0.621	0.316	0.674		3.5

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	3APY	2.09	47.07	40515	2157	98.68	0.1838	0.1817	0.2239	RANDOM	34.665

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]
0.85			1.27		-2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.433
r_dihedral_angle_4_deg	23.427
r_dihedral_angle_3_deg	16.06
r_dihedral_angle_1_deg	6.225
r_angle_refined_deg	1.618
r_angle_other_deg	0.532
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.433
r_dihedral_angle_4_deg	23.427
r_dihedral_angle_3_deg	16.06
r_dihedral_angle_1_deg	6.225
r_angle_refined_deg	1.618
r_angle_other_deg	0.532
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4547
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	160

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
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.