Experiment: 6TPR

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	100 mM Sodium citrate, 200 mM Ammonium acetate, 3% (v/v) MPD

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.754	α = 90
b = 118.754	β = 90
c = 115.242	γ = 120

Symmetry
Space Group	P 65 2 2

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-F		2018-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.2	115.242	99.9	0.234	0.98	6.6	13.5		8390

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.42	99.7		1.392	0.982		14

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6q7w, 4jvc	3.2	115.24	8357	413	99.916	0.208	0.2066	0.2419	RANDOM	125.861

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]
4	2		4		-12.976

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.45
r_lrange_it	19.136
r_dihedral_angle_3_deg	18.503
r_dihedral_angle_4_deg	16.792
r_scangle_it	13.701
r_mcangle_it	13.162
r_scbond_it	8.851
r_dihedral_angle_1_deg	8.393
r_mcbond_it	8.357
r_angle_refined_deg	1.289

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.45
r_lrange_it	19.136
r_dihedral_angle_3_deg	18.503
r_dihedral_angle_4_deg	16.792
r_scangle_it	13.701
r_mcangle_it	13.162
r_scbond_it	8.851
r_dihedral_angle_1_deg	8.393
r_mcbond_it	8.357
r_angle_refined_deg	1.289
r_nbtor_refined	0.309
r_nbd_refined	0.278
r_symmetry_nbd_refined	0.272
r_symmetry_xyhbond_nbd_refined	0.175
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.085
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1594
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	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 R01GM133198.