Experiment: 5IY5

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	8	277	15mM sodium phosphate, pH 8.0, 0.7% fluorinated octylmaltoside, 0.2% decylmaltoside, 3% ethylene glycol, 5% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3.55	65.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.29	α = 90
b = 183.872	β = 102.12
c = 148.929	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	CCD	RAYONIX MX300HE		2015-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	50	99.5	0.096	0.105	0.044	8.8	4.9		397399

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	2.02	99.5		0.599	0.623		3.7	9885

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	2DYR and 1HRC	2	40	377338	19990	99.4	0.1686	0.1665	0.2074	RANDOM	48.152

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]
-1.78		0.24	3.62		-1.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.558
r_dihedral_angle_4_deg	16.908
r_dihedral_angle_3_deg	16.469
r_sphericity_bonded	7.54
r_dihedral_angle_1_deg	6.584
r_scbond_it	4.651
r_mcangle_it	4.485
r_mcbond_it	3.204
r_angle_refined_deg	2.205
r_chiral_restr	0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.558
r_dihedral_angle_4_deg	16.908
r_dihedral_angle_3_deg	16.469
r_sphericity_bonded	7.54
r_dihedral_angle_1_deg	6.584
r_scbond_it	4.651
r_mcangle_it	4.485
r_mcbond_it	3.204
r_angle_refined_deg	2.205
r_chiral_restr	0.15
r_bond_refined_d	0.026
r_gen_planes_refined	0.024

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	30158
Nucleic Acid Atoms
Solvent Atoms	2237
Heterogen Atoms	2183

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.