Experiment: 6VJK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SWE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	21% PEG 3350, 8% glycerol, 100 mM Bis-Tris-Cl pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.26	α = 90
b = 79.549	β = 90
c = 281.549	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 PILATUS 300K		2018-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.98	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.6	50.0005	98.7	0.133	0.133	0.142	0.048	0.994	13	8.1		176700			16.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69	99.4		0.747	0.747	0.793	0.262	0.814	5.4	8.1

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1SWE	1.6	50	176551	8889	98.462	0.186	0.1841	0.2153	20.982

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]
-0.333			0.885		-0.552

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.722
r_dihedral_angle_4_deg	12.158
r_dihedral_angle_3_deg	10.601
r_dihedral_angle_1_deg	6.43
r_lrange_it	5.733
r_scangle_it	3.304
r_mcangle_it	2.545
r_scbond_it	2.196
r_mcbond_it	1.641
r_angle_refined_deg	1.324

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.722
r_dihedral_angle_4_deg	12.158
r_dihedral_angle_3_deg	10.601
r_dihedral_angle_1_deg	6.43
r_lrange_it	5.733
r_scangle_it	3.304
r_mcangle_it	2.545
r_scbond_it	2.196
r_mcbond_it	1.641
r_angle_refined_deg	1.324
r_nbtor_refined	0.282
r_symmetry_nbd_refined	0.164
r_nbd_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.123
r_chiral_restr	0.076
r_xyhbond_nbd_refined	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10826
Nucleic Acid Atoms
Solvent Atoms	1667
Heterogen Atoms	192

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	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 R01GM157729.