Experiment: 5IY5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DYR	2DYR and 1HRC
experimental model	PDB	1HRC	2DYR and 1HRC

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.17	0.2074	0.21	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 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.