Experiment: 4YRB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YR9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	283	0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris, 20%(w/v) Polyethylene glycol monomethyl ether 2000

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.24	α = 90
b = 154.05	β = 90
c = 199.19	γ = 90

Symmetry
Space Group	P 2 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	CCD	ADSC QUANTUM 315r		2014-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97911	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.25	121.859	97.4	0.134	0.153	0.073	8.6	4	35778	35778

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.25	3.43	94.3		0.566	0.566	0.325	1.3	3.5	4952

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	4YR9	3.25	47.12	33952	1772	96.97	0.2305	0.2276	0.2851	RANDOM	76.453

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]
			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.197
r_dihedral_angle_3_deg	16.004
r_dihedral_angle_4_deg	13.409
r_dihedral_angle_1_deg	5.852
r_mcangle_it	4.631
r_mcbond_it	2.724
r_mcbond_other	2.723
r_angle_refined_deg	1.06
r_angle_other_deg	0.716
r_chiral_restr	0.055

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.197
r_dihedral_angle_3_deg	16.004
r_dihedral_angle_4_deg	13.409
r_dihedral_angle_1_deg	5.852
r_mcangle_it	4.631
r_mcbond_it	2.724
r_mcbond_other	2.723
r_angle_refined_deg	1.06
r_angle_other_deg	0.716
r_chiral_restr	0.055
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10592
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	264

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
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.