Experiment: 6VJL

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	294.15	28% PEG 4000, 0.15 M ammonium sulfate, 50 mM Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.772	α = 90
b = 57.772	β = 90
c = 184.419	γ = 90

Symmetry
Space Group	I 41 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 PILATUS3 S 6M		2017-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim 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	50	99.9	0.073	0.073	0.076	1	19.6	11		39166

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)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.33	99.2		0.0101	0.0101	1.11	0.577		5.6

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	THROUGHOUT	1SWE	1.3	37.35	38946	2002	99.872	0.191	0.19	0.2009	19.813

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]
0.231			0.231		-0.462

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.805
r_dihedral_angle_3_deg	10.932
r_dihedral_angle_4_deg	10.378
r_lrange_it	7.333
r_dihedral_angle_1_deg	6.593
r_scangle_it	4.168
r_mcangle_it	2.92
r_scbond_it	2.762
r_mcbond_it	1.911
r_angle_refined_deg	1.336

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.805
r_dihedral_angle_3_deg	10.932
r_dihedral_angle_4_deg	10.378
r_lrange_it	7.333
r_dihedral_angle_1_deg	6.593
r_scangle_it	4.168
r_mcangle_it	2.92
r_scbond_it	2.762
r_mcbond_it	1.911
r_angle_refined_deg	1.336
r_nbtor_refined	0.284
r_symmetry_nbd_refined	0.151
r_nbd_refined	0.15
r_chiral_restr	0.083
r_symmetry_xyhbond_nbd_refined	0.072
r_xyhbond_nbd_refined	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	918
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	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.