Experiment: 6TBX

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	294	2-2.5M sodium acetate, 0.1M sodium citrate, pH 5

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.677	α = 90
b = 90.779	β = 115.65
c = 82.81	γ = 90

Symmetry
Space Group	P 1 21 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		2016-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

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	1.3	45.39	96.2	0.069	0.094	0.053	0.989	8.3	3		234209			11.4

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	1.3	1.37	94.1		0.447	0.64	0.37	0.803	2.4	2.8

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	5JDC	1.3	41.83	222393	11767	96.03	0.1277	0.126	0.1594	RANDOM	17.12

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]
-0.03		-0.02	-0.07		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.042
r_dihedral_angle_4_deg	18.427
r_dihedral_angle_3_deg	12.029
r_rigid_bond_restr	6.793
r_dihedral_angle_1_deg	6.242
r_angle_refined_deg	1.842
r_angle_other_deg	1.663
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.042
r_dihedral_angle_4_deg	18.427
r_dihedral_angle_3_deg	12.029
r_rigid_bond_restr	6.793
r_dihedral_angle_1_deg	6.242
r_angle_refined_deg	1.842
r_angle_other_deg	1.663
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7230
Nucleic Acid Atoms
Solvent Atoms	749
Heterogen Atoms	270

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
SCALA	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.