Experiment: 5LYG

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	20% PEG 3350 and 0.2M Sodium malonate dibasic monohydrate

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.73	α = 90
b = 127.22	β = 90
c = 39.38	γ = 90

Symmetry
Space Group	P 21 21 2

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 PILATUS3 S 6M		2015-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.979	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.52	39.4	98.9	0.052	0.999	12.29	3.4		67598		-3	29.811

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	1.52	1.56	95.1		1.016	0.471	1.06

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.6	39.38	29501	1625	99.67	0.1895	0.1886	0.2058	RANDOM	23.514

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]
			-0.23		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.041
r_sphericity_free	12.037
r_dihedral_angle_3_deg	11.996
r_dihedral_angle_4_deg	10.66
r_sphericity_bonded	5.917
r_dihedral_angle_1_deg	5.486
r_angle_refined_deg	0.948
r_rigid_bond_restr	0.502
r_chiral_restr	0.062
r_bond_refined_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.041
r_sphericity_free	12.037
r_dihedral_angle_3_deg	11.996
r_dihedral_angle_4_deg	10.66
r_sphericity_bonded	5.917
r_dihedral_angle_1_deg	5.486
r_angle_refined_deg	0.948
r_rigid_bond_restr	0.502
r_chiral_restr	0.062
r_bond_refined_d	0.005
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1516
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
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 R01GM133198.