Experiment: 5Y6K

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4X1B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	298	PIPES-Na 0.1M pH 6.6, disodium malonate 8mM, PEG 3350 17%, glycerol 18%

Crystal Properties
Matthews coefficient	Solvent content
3.84	67.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.012	α = 90
b = 155.752	β = 90
c = 107.554	γ = 90

Symmetry
Space Group	C 2 2 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		2014-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.93001	SSRF	BL17U1

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	2.85	103.29	99.7	0.078	0.084	0.029	9.8	8		27148

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	2.95	100		0.794	0.848	0.296	0.905		8.1

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	4X1B	2.86	103.29	25317	1283	97.48	0.1576	0.1537	0.2352	RANDOM	63.835

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]
-3.82			1.84		1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	62.931
r_dihedral_angle_2_deg	35.643
r_dihedral_angle_3_deg	17.343
r_dihedral_angle_4_deg	15.959
r_dihedral_angle_1_deg	5.951
r_rigid_bond_restr	3.851
r_angle_refined_deg	1.381
r_angle_other_deg	1.019
r_chiral_restr	0.078
r_bond_refined_d	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	62.931
r_dihedral_angle_2_deg	35.643
r_dihedral_angle_3_deg	17.343
r_dihedral_angle_4_deg	15.959
r_dihedral_angle_1_deg	5.951
r_rigid_bond_restr	3.851
r_angle_refined_deg	1.381
r_angle_other_deg	1.019
r_chiral_restr	0.078
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4997
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	77

Software

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

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.