Experiment: 6VZK

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	PEG 6000, 50 mM HEPES, 3-Aminobenzene-sulfonic acid, 5-Sulfosalicylic acid dihydrate, p-Coumaric acid, PIPES, Terephthalic acid, Vanillic acid

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.147	α = 90
b = 56.928	β = 90
c = 97.461	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 R 200K-A	Rigaku VariMax HF	2019-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.55	50	99.9	0.195	0.215	0.093	3.5	5.5		8711

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.75	100		0.489	0.864		5.2

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	3SOA	2.55	43.2	8711	446	99.81	0.2142	0.2103	0.2944	RANDOM	34.924

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]
0.91			-2.43		1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.242
r_dihedral_angle_4_deg	22.288
r_dihedral_angle_3_deg	19.46
r_dihedral_angle_1_deg	8.705
r_angle_refined_deg	1.589
r_angle_other_deg	1.198
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.242
r_dihedral_angle_4_deg	22.288
r_dihedral_angle_3_deg	19.46
r_dihedral_angle_1_deg	8.705
r_angle_refined_deg	1.589
r_angle_other_deg	1.198
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2075
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

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.