Experiment: 5U09

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V2Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5.5	293	31% PEG400, 100mM Sodium Citrate pH5.5, 100mM magnesium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.652	α = 90
b = 80.381	β = 91.72
c = 81.178	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		2016-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.6	50.01	96.9	0.194	5.6	5.4		19781

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	2.6	2.69	96.8		1.411	0.69		5.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3V2Y	2.6	50.01	11084	612	57.88	0.1832	0.1803	0.2382	RANDOM	44.12

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]
6.05		1.27	-2.83		-3.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.488
r_dihedral_angle_4_deg	20.71
r_dihedral_angle_3_deg	18.966
r_dihedral_angle_1_deg	8.654
r_mcangle_it	6.886
r_mcbond_it	4.549
r_mcbond_other	4.547
r_angle_refined_deg	1.2
r_angle_other_deg	0.643
r_chiral_restr	0.249

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.488
r_dihedral_angle_4_deg	20.71
r_dihedral_angle_3_deg	18.966
r_dihedral_angle_1_deg	8.654
r_mcangle_it	6.886
r_mcbond_it	4.549
r_mcbond_other	4.547
r_angle_refined_deg	1.2
r_angle_other_deg	0.643
r_chiral_restr	0.249
r_gen_planes_refined	0.012
r_bond_refined_d	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3762
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	119

Software

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

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.